Reaction mixture for pyrophosphorolysis activated polymerization (PAP)

ABSTRACT

A novel method of pyrophosphorolysis activated polymerization (PAP) has been developed. In PAP, pyrophosphorolysis and polymerization by DNA polymerase are coupled serially for each amplification by using an activatable oligonucleotide P* that has a non-extendible 3′-deoxynucleotide at its 3′ terminus. PAP can be applied for exponential amplification or for linear amplification. PAP can be applied to amplification of a rare allele in admixture with one or more wild-type alleles by using an activatable oligonucleotide P* that is an exact match at its 3′ end for the rare allele but has a mismatch at or near its 3′ terminus for the wild-type allele. PAP is inhibited by a mismatch in the 3′ specific sequence as far as 16 nucleotides away from the 3′ terminus. PAP can greatly increase the specificity of detection of an extremely rare mutant allele in the presence of the wild-type allele. Specificity results from both pyrophosphorolysis and polymerization since significant nonspecific amplification requires the combination of mismatch pyrophosphorolysis and misincorporation by the DNA polymerase, an extremely rare event. Using genetically engineered DNA polymerases greatly improves the efficiency of PAP.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application is a continuation of U.S. patent applicationSer. No. 11/772,622 filed 2 Jul. 2007, now U.S. Pat. No. 7,504,221,which in turn is a continuation of U.S. patent application Ser. No.10/798,844 filed 12 Mar. 2004, now U.S. Pat. No. 7,238,480, which inturn is a continuation of U.S. patent application Ser. No. 10/434,369filed 9 May 2003, now U.S. Pat. No. 7,033,763, which in turn is acontinuation-in-part of U.S. patent application Ser. No. 10/269,879filed on 15 Oct. 2002, now U.S. Pat. No. 7,105,298, which in turn is adivision of U.S. patent application Ser. No. 09/789,556 filed on 22 Feb.2001, now U.S. Pat. No. 6,534,269. Application Ser. No. 09/789,556 isfurther related to and claims priority under 35 USC §119(e) to U.S.provisional patent application Ser. Nos. 60/184,315 filed on 23 Feb.2000, 60/187,035 filed on 6 Mar. 2000 and 60/237,180 filed on 3 Oct.2000. Application Ser. No. 10/434,369 is further related to and claimspriority under 35 USC §119(e) to U.S. provisional patent applicationSer. No. 60/379,092 filed on 10 May 2002. Each of these applications isincorporated herein by reference.

BACKGROUND OF THE INVENTION

This invention relates to nucleic acid polymerization and amplification.In particular, it relates to a novel and general method for nucleic acidamplification, in which pyrophosphorolysis and polymerization areserially-coupled. The method has been adapted for allele-specificamplification and can greatly increase the specificity to detect anextremely rare allele in the presence of wild-type alleles. We refer tothe method as pyrophosphorolysis activated polymerization (PAP).

The publications and other materials used herein to illuminate thebackground of the invention or provide additional details respecting thepractice, are incorporated by reference, and for convenience arerespectively grouped in the appended Bibliography.

Multiple methods for detecting mutations present in less than 10% ofcells (i.e. rare alleles) have been developed, including PCRamplification of specific alleles (PASA), peptide nucleic acid (PNA)clamping blocker PCR, allele-specific competitive blocker PCR, mismatchamplification mutation assay (MAMA), restriction fragment-lengthpolymorphism (RFLP)/PCR (Parsons and Heflich, 1997) and QE-PCR (Ronaiand Minamoto, 1997). These methods: i) amplify the rare alleleselectively, ii) destroy the abundant wild-type allele, or iii)spatially separate the rare allele from the wild-type allele. Thespecificity achievable under typical research/clinical conditions is10⁻³ (Parsons and Heflich, 1997), although a few publications reportedhigher specificity of detection (Pourzand and Cerutti, 1993; Knoll etal., 1996). These methods either do not generally achieve the higherspecificity or are not suitable for routine analysis.

A robust method of detecting one mutant allele in 10⁴-10⁹ wild-typealleles would be advantageous for many applications including detectingminimal residual disease (recurrence after remission or rare remainingcancer cells in lymph nodes and other neighboring tissues) andmeasurement of mutation load (the frequency and pattern of somaticmutations present in normal tissues). Individuals with a high mutationload may be at increased risk for cancer due to either environmentalexposure or endogenous defects in any of hundreds of genes necessary tomaintain the integrity of the genome. For those individuals found tohave a high mutation load, clues to etiology can be obtained by definingthe mutation pattern.

There are many DNA sequencing methods and their variants, such as theSanger sequencing using dideoxy termination and denaturing gelelectrophoresis (Sanger et al., 1977), Maxam-Gilbert sequencing usingchemical cleavage and denaturing gel electrophoresis (Maxam and Gilbert,1977), pyro-sequencing detecting pyrophosphate (PP_(i)) released duringthe DNA polymerase reaction (Ronaghi et al., 1998), and sequencing byhybridization (SBH) using oligonucleotides (Lysov et al., 1988; Bainsand Smith, 1988; Drmanac et al., 1989; Khrapko et al., 1989; Pevzner etal., 1989; Southern et al., 1992).

There are multiple gel-based methods for scanning for unknown mutationsincluding single stranded conformation polymorphism (SSCP) and theSSCP-hybrid methods of dideoxy fingerprinting (ddF), restrictionendonuclease fingerprinting (REF), and Detection Of Virtually AllMutations-SSCP (DOV AM-S), denaturing gradient gel electrophoresis(DGGE), denaturing HPLC (dHPLC) chemical or enzymatic cleavage (Sarkaret al., 1992; Liu and Sommer, 1995; Liu et al., 1999; Myers et al.,1985; Cotton et al., 1988; Liu et al., 1999; Buzin et al., 2000;Spiegelman et al., 2000). DOVAM-S and chemical cleavage reactions havebeen shown in blinded analyses to identify essentially all mutations(Buzin et al., 2000). dHPLC, which is based on reverse phasechromatography, also may identify essentially all mutations underappropriate conditions (O'Donovan et al., 1998; Oefner and Underhill,1998; Spiegelman et al., 2000). Efforts are under way to develop generalscanning methods with higher throughput.

Sequencing by hybridization (SBH) is being adapted to scanning orresequencing for unknown mutations on microarrays (Southern, 1996). Thiscontinues to be a promising area of intense study. However it is notpossible as yet to detect most microinsertions and deletions with thisapproach and the signal to noise ratio for single base changes precludesdetection of 5-10% of single nucleotide changes (Hacia, 1999).Alternative approaches warrant exploration.

It is becoming increasingly apparent that in vivo chromatin structure iscrucial for mammalian gene regulation and development. Stable changes inchromatin structure often involve changes in methylation and/or changesin histone acetylation. Somatically heritable changes in chromatinstructure are commonly called epigenetic changes (Russo and Riggs, 1996)and it is now clear that epigenetic “mistakes” or epimutations arefrequently an important contributing factor to the development of cancer(Jones and Laird, 1999).

One of the few methods for assaying in vivo chromatin structure, and theonly method with resolution at the single nucleotide level, isligation-mediated PCR (LM-PCR) (Mueller and Wold, 1989; Pfeifer et al.,1989) and its variant of terminal transferase-mediated PCR (TD-PCR)(Komura and Riggs, 1998). Many aspects of chromatin structure can bedetermined by LM-PCR, such as the location of methylated cytosineresidues, bound transcription factors, or positioned nucleosomes. It isreadily apparent that LM-PCR works better with some primer sets thanwith others. Thus, it is desired to develop a more robust method ofmeasuring chromatin structure.

Thus, it is an object of the present invention to develop alternativemethods for amplification of DNA, for sequencing DNA and for analysis ofchromatin structure. This object is accomplished by the use of the novelpyrophosphorolysis activated polymerization (PAP) as described herein.PAP has the potential to enhance dramatically the specificity of theamplification of specific alleles, for resequencing DNA and forchromatin structure analysis.

SUMMARY OF THE INVENTION

The invention is a pyrophosphorolysis activated polymerization (PAP)method of synthesizing a desired nucleic acid strand on a nucleic acidtemplate strand. The method comprises the following steps carried outserially.

(a) Annealing to the template strand a complementary activatableoligonucleotide P*. This activatable oligonucleotide has anon-extendible 3′ terminus that is activatable by pyrophosphorolysis(hereinafter referred to as a non-extendible 3′ terminus or a 3′non-extendible end or a non-extendible 3′ end). The non-extendible 3′terminus (or end) is a nucleotide or nucleotide analog which has thecapacity to form a Watson-Crick base bair with a complementarynucleotide and which lacks a 3′ OH capable of being extended by anucleic acid polymerase. In one embodiment, the non-extendible 3′terminus may be a non-extendible 3′ deoxynucleotide, such as adideoxynucleotide. In a second embodiment, the non-extendible 3′terminus may be a chemically modified nucleotide lacking the 3′ hydroxylgroup, such as an acyclonucleotide. Acyclonucleotides substitute a2-hydroxyethoxymethyl group for the 2′-deoxyribofuranosyl sugar normallypresent in dNMPs. In other embodiments, the non-extendible 3′ terminusmay be other blockers as described herein. In one embodiment, theactivatable oligonucleotide P* has no nucleotides at or near its 3′terminus that mismatch the corresponding nucleotides on the templatestrand. In a second embodiment, the activatable oligonucleotide P* has amismatch at or within 16 nucleotides of its 3′ terminus with respect toa corresponding nucleotide on the template strand. The terminal3′-deoxynucleotide is hybridized to the template strand when theoligonucleotide P* is annealed.

(b) Pyrophosphorolyzing the annealed activatable oligonucleotide P* withpyrophosphate and an enzyme that has pyrophosphorolysis activity. Thisactivates the oligonucleotide P* by removal of the hybridizednon-extendible 3′ terminus.

(c) Polymerizing by extending the activated oligonucleotide P* on thetemplate strand in presence of four nucleoside triphosphates of theiranalogs and a nucleic acid polymerase to synthesize the desired nucleicacid strand.

The PAP method can be applied to amplify a desired nucleic acid strandby the following additional steps.

(d) Separating the desired nucleic acid strand of step (c) from thetemplate strand, and

(e) Repeating steps (a)-(d) until a desired level of amplification ofthe desired nucleic acid strand is achieved.

In a preferred aspect, the PAP method as described above is applied toallele-specific amplification (PAP-A). In this application, the nucleicacid template strand is a sense or antisense strand of one allele and ispresent in admixture with the corresponding (sense or antisense) nucleicacid strand of the second allele (the allelelic strand). The activatableoligonucleotide P* has at least one nucleotide or analog at or near its3′ terminus, e.g., within 16 nucleotides of the 3′ terminus, thatmismatches the corresponding nucleotide of the allelic strand. Becauseof the mismatch, in step (a) of the PAP method the non-extendible 3′terminus of oligonucleotide P* is not substantially hybridized to theallelelic strand. In step (b) the pyrophosphorolysis does notsubstantially remove the non-hybridized non-extendible 3′ terminus fromthe activatable oligonucleotide P* annealed to the allelic strand. Instep (c) the oligonucleotide P* is not substantially extended bypolymerization on the allelic strand. As a result, the desired nucleicacid strand synthesized on the template strand is amplifiedpreferentially over any nucleic acid strand synthesized on the allelelicstrand.

In a second preferred aspect, the PAP-A method described above can beperformed bidirectionally (Bi-PAP-A). Bidirectional-PAP (Bi-PAP) is anovel design that preferably uses two opposing pyrophosphorolysisactivatable oligonucleotides (P*) with one nucleotide overlap at their3′ termini. Thus, in Bi-PAP, PAP-A is performed with a pair of opposingactivatable oligonucleotide P*s. Both the downstream and upstream P*sare specific for the nucleotide of interest at the 3′ termini (e.g., anA:T base pair). In the initial round of amplification from genomic DNA,segments of undefined size are generated. In subsequent rounds, asegment equal to the combined lengths of the oligonucleotides minus oneis amplified exponentially. Nonspecific amplification occurs at lowerfrequencies because this design eliminates misincorporation error froman unblocked upstream. The P*s may be 30-60 nucleotides for mostefficient amplification.

The PAP method can be used to amplify either RNA or DNA. When used toamplify DNA, the activatable oligonucleotide P* may be a2′-deoxyoligonucleotide, the non-extendible 3′ terminus may be, e.g., a2′,3′-dideoxynucleotide or an acyclonucleotide or other blockers asdescribed herein, the four nucleoside triphosphates are2′-deoxynucleoside triphosphates or their analogs, and the nucleic acidpolymerase is a DNA polymerase. The DNA polymerase used in step (c) canalso be the enzyme having pyrophosphorolysis activity used in step (b).Preferred DNA polymerases having pyrophosphorolysis activity arethermostable Tfl, Taq, and genetically engineered DNA polymerases, suchas AmpliTaqFs and ThermoSequenase™. These genetically engineered DNApolymerases have the mutation F667Y or an equivalent mutation in theiractive sites. The use of genetically engineered DNA polymerases, such asAmpliTaqFs and ThermoSequenase™, greatly improves the efficiency of PAP.These Family I DNA polymerases can be used when the activatableoligonucleotide P* is a 3′ dideoxynucleotide or an acyclonucleotide.When the activatable oligonucleotide P* is an acyclonucleotide, FamilyII archaeon DNA polymerases can also be used. Examples of suchpolymerases include, but are not limited to, Vent (exo-) and Pfu (exo-).These polymerases efficiently amplify 3′acyclonucleotide blocked P*. Twoor more polymerases can also be used in one reaction. If the template isRNA, the nucleic acid polymerase may be RNA polymerase, reversetranscriptase, or their variants. The activatable oligonucleotide P* maybe a ribonucleotide or a 2′-deoxynucleotide. The non-extendible 3′terminus may be a 3′ deoxyribonucleotide or an acyclonucleotide. Thefour nucleoside triphosphates may be ribonucleoside triphosphates, 2′deoxynucleoside triphosphates or their analogs. For convenience, thedescription that follows uses DNA as the template. However, RNA is alsoincluded, such as described for the present aspect.

Amplification by the PAP method can be linear or exponential. Linearamplification is obtained when the activatable oligonucleotide P* is theonly complementary oligonucleotide used. Exponential amplification isobtained when a second opposing oligonucleotide, which may be a P*, ispresent that is complementary to the desired nucleic acid strand. Theactivatable oligonucleotide P* and the second oligonucleotide flank theregion that is targeted for amplification. In step (a) the secondoligonucleotide anneals to the separated desired nucleic acid strandproduct of step (d). In step (c) polymerization extends the secondoligonucleotide on the desired nucleic acid strand to synthesize a copyof the nucleic acid template strand. In step (d) the synthesized nucleicacid template strand is separated from the desired nucleic acid strand.Steps (a) through (d) are repeated until the desired level exponentialamplification has been achieved.

In the PAP method, a mismatch between the activatable oligonucleotide P*and the template strand results in no substantial amplification, if themismatch occurs in the 3′ specific subsequence of P* at the 3′ terminusof P* or within 16 nucleotides of the 3′ terminus of P*. This lack ofamplification for such mismatches in the 3′ specific subsequence of P*provides four billion different and specific oligonucleotides with onebase substitution resolution.

In a preferred aspect, the PAP method is used for exponentialamplification of a rare, mutant allele in a mixture containing one ormore wild-type alleles. Strands of the alleles are separated to providesingle-stranded nucleic acid, and then the following steps are carriedout serially.

(a) Annealing to the sense or antisense strands of each allele acomplementary activatable 2′-deoxyoligonucleotide P* that has anon-extendible 3′ terminus. The non-extendible 3′ terminus may be, e.g.,a non-extendible 2′,3′-dideoxynucleotide or an acyclonucleotide. P* hasno 2′-deoxynucleotides at or near its 3′ terminus that mismatch thecorresponding 2′-deoxynucleotides on the mutant strand, but has at leastone 2′-deoxynucleotide at or near its 3′ terminus that mismatches thecorresponding 2′-deoxynucleotide on the wild-type stand. Consequently,the non-extendible 3′ terminus is hybridized to the mutant strand butnot to the wild-type strand when the oligonucleotide P* is annealed.Simultaneously, a second 2′-deoxyoligonucleotide that is complementaryto the anti-parallel strands of each allele is annealed to theanti-parallel strands. The activatable 2′-deoxyoligonucleotide P* andthe second 2′-deoxyoligonucleotide flank the region of the gene to beamplified.

(b) Pyrophosphorolyzing the activatable 2′-deoxyoligonucleotide P* thatis annealed to a mutant strand with pyrophosphate and an enzyme that haspyrophosphorolysis activity. This activates the 2′-deoxyoligonucleotideP* that is annealed to the mutant strand by removal of the hybridizednon-extendible 3′ terminus. It does not substantially activate the2′-deoxyoligonucleotide P* when it is annealed to the mutant strandbecause the non-hybridized non-extendible 3′ terminus is notsubstantially removed by the pyrophosphorolysis.

(c) Polymerizing by extending the activated oligonucleotide P* on themutant strand in presence of four nucleoside triphosphates or theiranalogs and a DNA polymerase and extending the second2′-deoxyoligonucleotide on both mutant and wild-type anti-parallelstrands.

(d) Separating the extension products of step (c);

(e) Repeating steps (a)-(d) until the desired level of amplification ofthe mutant allele has been achieved.

The activatable 2′-deoxyoligonucleotide P* is annealed to the antisensestrands of the alleles and the second 2′-deoxyoligonucleotide isannealed to the sense strands, or vice versa.

Steps (a) to (c) of PAP can be conducted sequentially as two or moretemperature stages on a thermocycler, or they can be conducted as onetemperature stage on a thermocycler.

Nucleoside triphosphates and 2′-deoxynucleoside triphosphates or theirchemically modified versions may be used as substrates formultiple-nucleotide extension by PAP, i.e., when one nucleotide isincorporated the extending strand can be further extended.2′,3′-dideoxynucleoside triphosphates, their chemically modifiedversions, acyclonucleotides or other blocked nucleotides which areterminators for further extension may be used for single-nucleotideextension. 2′,3′-dideoxynucleoside triphosphates may be labeled withradioactivity or dye for differentiation from the 3′ terminaldideoxynucleotide, if present, of oligonucleotide P*. Mixtures ofnucleoside triphosphates or 2′-deoxynucleotide triphosphates or theiranalogs, and 2′,3′-dideoxynucleoside triphosphates or their analogs mayalso be used.

PAP can be used in a novel method of DNA sequence determination. In PAP,pyrophosphorolysis and polymerization by DNA polymerase are coupledserially by using P*, an oligonucleotide containing a non-extendible 3′terminus. The non-extendible 3′ terminus may be, e.g., a non-extendible3′-deoxynucleotide or an acyclonucleotide. This principle is based onthe specificity of PAP and in turn on the base pairing specificity ofthe 3′ specific subsequence. This property of the 3′ specificsubsequence can be applied to scan or resequence for unknown sequencevariants, to determine de novo DNA sequence, to compare two DNAsequences, and to monitor gene expression profiling in large scale. A P*array is possible in these methods. That is, each of the P*s can beimmobilized at an individual dot or a solid support, thus allowing allthe PAP reactions to be processed in parallel.

Thus in one aspect, the PAP method is used for scanning or resequencingunknown sequence variants within a predetermined sequence by carryingout the following steps serially.

(a) Mixing under hybridization conditions a template strand of thenucleic acid with multiple sets of four activatable oligonucleotides P*which are sufficiently complementary to the template strand to hybridizetherewith. Within each set the oligonucleotides P* differ, from eachother in having a different non-extendible 3′ terminus, so that thenon-extendible 3′ terminus is hybridized to the template strand if thetemplate strand is complementary to the non-extendible 3′ terminus. Thenumber of sets corresponds to the number of nucleotides in the sequence.The non-extendible 3′ terminus may be, e.g., a non-extendible3′-deoxynucleotide or an acyclonucleotide.

(b) Treating the resulting duplexed P*s with pyrophosphate and an enzymethat has pyrophosphorolysis activity to activate by pyrophosphorolysisonly those oligonucleotides P* which have a non-extendible 3′ terminusthat is hybridized to the template strand.

(c) Polymerizing by extending the activated oligonucleotides P* on thetemplate strand in presence of four nucleoside triphosphates or theiranalogs and a nucleic acid polymerase.

(d) Separating the nucleic acid strands synthesized in step (c) from thetemplate strand.

(e) Repeating steps (a)-(d) until a desired level of amplification isachieved, and

(f) Arranging the nucleic acid sequence in order by analyzing overlapsof oligonucleotides P* that produced amplifications.

In a second aspect, the PAP method is used for determining de novo thesequence of a nucleic acid by carrying out the following steps serially.

(a) Mixing under hybridization conditions a template strand of thenucleic acid with multiple activatable oligonucleotides P*. All of theoligonucleotides P* have the same number n of nucleotides as thetemplate and constitute collectively all possible sequences having nnucleotides. All of the oligonucleotides P* have a non-extendible 3′terminus. The non-extendible 3′ terminus may be, e.g., a non-extendible3′-deoxynucleotide or an acyclonucleotide. Any oligonucleotides P* thatare sufficiently complementary will hybridize to the template strand.The non-extendible 3′ terminus will hybridize to the template strandonly if the template strand is complementary at the positioncorresponding to the 3′ terminus.

(b) Treating the resulting duplexed P*s with pyrophosphate and an enzymethat has pyrophosphorolysis activity to activate only those hybridizedoligonucleotides P* which have a non-extendible 3′ terminus that ishybridized to the template strand, by pyrophosphorolysis of thosehybridized non-extendible 3′ termini.

(c) Polymerizing by extending the activated oligonucleotides P* on thetemplate strand in presence of four nucleoside triphosphates or theiranalogs and a nucleic acid polymerase.

(d) Separating the nucleic acid strands synthesized in step (c) from thetemplate strand.

(e) Repeating steps (a)-(d) until a desired level of amplification hasbeen achieved, and

(f) Determining the sequence of oligonucleotides P* that producedamplifications, then arranging the nucleic acid sequence in order byanalyzing overlaps of these oligonucleotides.

PAP can also be used to study chromatin structure analogously toligation-mediated PCR (LM-PCR) by carrying out the following stepsserially. LM-PAP has been used for the determination of primarynucleotide sequence, cytosine methylation patterns, DNA lesion formationand repair and in vivo protein-DNA footprints (Dai et al., 2000; Muellerand Wold, 1989; Pfeifer et al., 1989; Pfeifer et al., 1999; Becker andGrossman, 1993). Ligation-mediated PAP (LM-PAP) involves cleavage,primer extension, linker ligation and PAP that can be applied foranalysis of in vivo chromatin structure, such as, methylated state ofchromosomes, and for other nucleic acid analysis as for LM-PCR.

The nature of LM-PAP is that the template is synthesized before PAP,such as by ligation reaction or by extension using terminal transferase.PAP may be any type of PAP: with only one P*, with two opposingoligonucleotides where at least one is P*, Bi-PAP, matched PAP,mismatched PAP, and so on. Thus, at its simplest, LM-PAP is theapplication of PAP to a presynthesized template. LM-PAP may be performedby steps (i), (ii), (iii), (iv) and (v), by steps (i), (ii), (iii) and(vi), by steps (ii), (iii), (iv) and (v) or by steps (ii), (iii) and(vi), where the steps are as follows.

(i) The cleavage occurs chemically, enzymatically or naturally to“breakdown” nucleic acid strands. The nucleic acid usually is genomicDNA that may have lesions or nicks produced in vivo.

(ii) The oligonucleotide P1 is gene-specific and its extensionincludes: 1) annealing to the template strand a substantiallycomplementary oligonucleotide; 2) extending the oligonucleotide on thetemplate strand in the presence of nucleoside triphosphates or theiranalogs and a nucleic acid polymerase, the extension “runs off” at thecleavage site on the template strand. Steps 1) and 2) may be repeated.

The primer extension may be replaced by a P* extension, in which theabove PAP is performed with only one activatable oligonucleotide P*.

(iii) The linker ligation step includes ligation of a linker to the 3′terminus of the synthesized nucleic acid strand. The linker ligationstep may be replaced by a terminal transferase extension that isnon-template dependent polymerization and an extra nucleic acid sequenceis added to the 3′ terminus of the synthesized nucleic acid strand.

(iv) PCR is performed with a second gene-specific oligonucleotide (P2)together with an oligonucleotide specific for the linker or the addedsequence by terminal transferase.

(v) A third gene-specific P* (P3) is used to detect the PCR generatedfragments. PAP method is applied with only one activatableoligonucleotide P*. The extension of the activated oligonucleotide P*“runs off” at the end of the template strand generated in IV. The PAPmethod may be applied in an allele-specific manner. The activatableoligonucleotide P* may contain one or more nucleotides that are notcomplementary to the template strand. The uncomplimentary nucleotide(s)of P* may locate at the 3′ terminus of P*.

(vi) Instead of steps (iv) and (v), PAP method can be applied with twoopposing oligonucleotides of which at least one is the activatableoligonucleotide P*. The activatable oligonucleotide P*(P3) isgene-specific. The second oligonucleotide is specific for the linker orthe added sequence by terminal transferase. The second oligonucleotidemay be another activatable oligonucleotide P* or a regularoligonucleotide. The PAP method may be applied in an allele-specificmanner. The activatable oligonucleotide P* (P3) may contain one or morenucleotides that are not complementary to the template strand. Theuncomplimentary nucleotide(s) of P* may locate at the 3′ terminus of P*(P3).

The third gene-specific oligonucleotide (P3) is then usually used tolabel and allow visualization of the PCR generated fragments. P3 islabeled at the 5′ terminus with ³²P or, more recently, with nearinfrared fluorochromes such as IRD 700 or IRD 800 (Li-Cor Inc.) (Dai etal., 2000).

PAP can be used to detect a target nucleic acid. In one embodiment thismethod involves the following steps:

(a) adding to a nucleic acid containing sample an oligonucleotide P*,wherein the oligonucleotide P* has a non-extendible 3′ terminus, whereinthe 3′ terminal residue of oligonucleotide P* is removable bypyrophosphorolysis, and wherein the oligonucleotide P* anneals to asubstantially complementary strand of the target nucleic acid present inthe sample;

(b) removing the 3′ non-extendible terminus of the oligonucleotide P*annealed to the substantially complementary strand of the target nucleicacid by pyrophosphorolysis to unblock the oligonucleotide P* to producean unblocked oligonucleotide; and

(c) detecting the presence of the target nucleic acid, wherein thesequence of the target nucleic acid is substantially complementary tothe sequence of the oligonucleotide P*.

The method of the first embodiment may further include before thedetection step the step: (b1) extending the unblocked oligonucleotideusing a nucleic acid polymerase to produce an extended oligonucleotide.The method may also include the addition of a second oligonucleotidewhich may or may not have a 3′ non-extendible terminus. The secondoligonucleotide may anneal to the substantially complementary strand ofthe target nucleic acid or it may anneal to the complement of thesubstantially complementary strand of the target nucleic acid.

In a second embodiment for detecting a nucleic acid the method involvesthe following steps:

(a) adding to a nucleic acid containing sample two oligonucleotide P*s,wherein each oligonucleotide P* has a non-extendable 3′ terminus,wherein the 3′ terminal residue of each oligonucleotide P* is removableby pyrophosphorolysis, wherein one oligonucleotide P* overlaps with theother oligonucleotide P* by at least one nucleotide at their respective3′ ends, and wherein one oligonucleotide P* anneals to a substantiallycomplementary strand of the target nucleic acid present in the sampleand the other oligonucleotide P* anneals to a complement of thesubstantially complementary strand of the target nucleic acid;

(b) removing the 3′ non-extendable terminus of the oligonucleotide P*sannealed to the target nucleic acid by pyrophosphorolysis to unblock theoligonucleotide P*s to produce unblocked oligonucleotides; and

(c) detecting the presence of the target nucleic acid, wherein thesequence of the target nucleic acid is substantially complementary tothe sequence of the oligonucleotide P*s.

The method of the second embodiment may further include before thedetection step the step: (b1) extending the unblocked oligonucleotideusing a nucleic acid polymerase to produce an extended oligonucleotide.

In one embodiment, the detection of the nucleic acid in step (c) isperformed by detecting the unblocking of oligonucleotide P*. In oneaspect, the unblocking is detected by loss of a label contained in the3′ terminal residue of oligonucleotide P*. In a second aspect, theunblocking is detected by detecting the presence of a 3′ OH on the 3′terminal residue that is capable of extension or ligation. In thisaspect, the detection is determined by extending the unblockedoligonucleotide or by ligating the unblocked oligonucleotide to anoligonucleotide. In a second embodiment, the detection of the nucleicacid in step (c) is performed by detecting the extended oligonucleotide.In one aspect, the extended oligonucleotide is detected by the presenceof a label in the extended oligonucleotide. The label is part of anucleotide or nucleotide analog used in the extension step. In a secondaspect, the extended oligonucleotide is detected by gel electrophoresis.In a third aspect, the extended oligonucleotide is detected by thebinding or incorporation of a dye or spectral material.

The P* oligonucleotides are selected to be “substantially”complementary” to the different strands of each specific sequence to beamplified. Therefore, the P* oligonucleotide sequence need not reflectthe exact sequence of the template. For example, a non-complementarynucleotide segment may be attached to the 5′-end of the P*oligonucleotide, with the remainder of the P* oligonucleotide sequencebeing complementary to the strand. Alternatively, non-complementarybases or longer sequences can be interspersed into the P*oligonucleotide, provided that the P* oligonucleotide sequence hassufficient complementarity with the sequence of the strand to beamplified to hybridize therewith and form a template for synthesis ofthe extension product of the other P* oligonucleotide. The ability todetect nucleic acid sequences which are substantially complementary tooligonucleotide P* is particularly useful for the detection of multiplemutations, such as seen in high viral load, where the detection of thepresence of the virus is important and not necessarily the exact nucleicacid sequence of the virus. This method is also capable of detectingnucleic acids that are completely complementary.

The present invention also includes other modifications of PAP.

-   -   The activatable oligonucleotide P* may contain blocked        nucleotides at other positions in addition to the 3′ terminus.    -   The introduction of internal blocking nucleotides results in an        interface between amplification and PAP which would permit PAP        to amplify in a non-exponential manner (e.g., quadratic or        geometric) with higher fidelity, i.e., errors made by the        polymerase would not be propagatable.    -   The activatable oligonucleotide P* may contain modified        nucleotides that are extendible as well as the 3′ blocked        nucleotide. Thus, anywhere 5′ to the 3′ terminus, there may be        either blocking or non-blocking modified nucleotides.    -   A polymerase that pyrophosphorolyzes the mismatched primer        rather than the matched primer could be used to detect rare        mutations in which the P* that mismatched at the 3′ terminus is        activated and extended.    -   The detection of a rare mutation is based on no mismatch        anywhere along the length of the oligonucleotide because a        mismatch inhibits the activation of P*s.    -   Activation may occur by another mechanism, such as a 3′        exonuclease. The 3′ exonuclease may have specificity for the        matched primer or the mismatched primer so that it discriminates        as to whether there is a mismatch at the 3′ end. The 3′        exonuclease can be used either way. If it prefers a mismatch, it        can be used as described above, but its ability to detect        uncommon mutations would depend on some specificity for        activation, although that specificity may come partly from        internal mismatches.    -   The extension reaction can be performed by a DNA polymerase, an        RNA polymerase or a reverse transcriptase, the template may be a        DNA or an RNA, and the oligonucleotide P* may be a DNA, an RNA,        or a DNA/RNA heteromer.    -   Pyrophosphorolysis and the extension can be performed by        different polymerases. For example, the P* may include a        penultimate modified oligonucleotide that could not be extended        by pyrophosphorolyzing polymerase but could be extended by        another polymerase. One example is a 3′ dideoxy that could be        pyrophosphorolyzed by a DNA polymerase, but the presence of a        ribonucleotide in the penultimate position would require        extension by an RNA polymerase.    -   PAP can be generalized as an inactive oligonucleotide that is        activated by a nucleic acid metabolizing enzyme, such as        helicases, topoisomerases, telomerases, RNase H or restriction        enzymes.    -   Methylases would detect the presence or absence of a methyl        group in genomic DNA. Methylases could be coupled with        truncating amplification which forces the polymerase back to the        template.    -   A P* in which the 3′ end is a dideoxy and penultimate few        nucleotides are ribos can be used as a tool for differentially        making a protein product derived from a specific mutation that        was desired, or for making a protein product whose expression is        linked to the presence of a particular sequence.        Pyrophosphorolysis would activate the P* if there was a precise        match to the mutation at the 3′ end. The activated        oligonucleotide is then a substrate for the generation of RNA by        an RNA polymerase. The RNA could then be translated in vitro to        produce the protein product.    -   PAP (PAP, Bi-PAP, matched or mismatched PAP, simplex PAP,        multiplex PAP and others) can be used for quantification. The        yield of the amplification products is quantitatively associated        with the amount of input template. The association may be        proportional or otherwise.    -   In PAP, product may accumulate linearly, exponentially or        otherwise.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows a schematic of the detection of a rare mutation byallele-specific PAP (PAP-A).

FIG. 2 shows a schematic of bidirectional PAP-A (Bi-PAP-A).

FIG. 3 shows a schematic of PAP-based resequencing (PAP-R) performed ona microarray with programmable photochemical oligonucleotide.

FIG. 4 shows a schematic of microarray-based resequencing to detect a Gto A mutation.

FIG. 5 shows a schematic of ligation-mediated PCR (LM-PCR).

FIGS. 6A and 6B are a schematic illustrating use of PAP to detect the Gallele at nucleotide 229 of the D₁ dopamine receptor gene. The procedureis described in detail in Example 1 below.

FIG. 6C is an autoradiogram of PAP from the G/G, A/A and G/A genotypesof the human dopamine receptor gene.

FIGS. 7A and 7B are diagrams illustrating enhanced specificity of PAPrelative to PASA.

FIGS. 8A and 8B are autoradiograms showing the results ofelectrophoresis of samples obtained in Example 1 below.

FIG. 9 is an autoradiogram showing the results of electrophoresis ofsamples obtained in Example 1 below.

FIG. 10 is an autoradiogram showing the results of electrophoresis ofsamples obtained in Example 1 below.

FIG. 11A is a schematic illustrating enhancement of PAP efficiency.

FIG. 11B is an autoradiogram of PAP from the G/G, A/A and G/A genotypesof the human dopamine receptor gene.

FIGS. 12A-12E are autoradiograms showing the results of electrophoresisof samples obtained in Example 2 below.

FIG. 13 is an autoradiogram showing the results of electrophoresis ofsamples obtained in Example 2 below.

FIG. 14 is an autoradiogram showing the results of electrophoresis ofsamples obtained in Example 2 below.

FIG. 15 is an autoradiogram showing the results of electrophoresis ofsamples obtained in Example 3 below.

FIGS. 16A-16B show UV footprinting by LM-PAP. FIG. 16A showsallele-specific LM-PAP versus allele-specific LM-PCR for the dopamine D₁receptor gene. FIG. 16B shows LM-PAP for the pgk gene.

FIGS. 17A-17B show PAP amplification directly from human (FIG. 17A) andmouse (FIG. 17B) genomic DNA using PAP and Bi-PAP, respectively.

FIGS. 18A-18E show PAP amplification using 3′ terminal acyclonucleotideblocked P*. FIG. 18A: Model: A duplexed DNA template of the lacI gene isshown. The mutated template contains a G at the nucleotide position 369,while the wild-type template contains a T at the nucleotide position 369of the lacI gene. P*=pyrophosphorolysis activatable oligonucleotide. TheP* has an acycloNMP or a ddNMP at the 3′ terminus. The P* is specific tothe mutated template but mismatches to the wild-type template at the 3′terminus (Table 6). 0=oligodeoxynucleotide. PAP was performed with P*1and O1, P*2 and O2, or P*1 and P*2, respectively. FIG. 18B: PAP with 30mer P*s: The P*s are specific for the mutated template but mismatch thewild-type template at their 3′ terminus. In lanes 1-8 are 3′ terminalacyclonucleotide blocked P*s. In lanes 9-16 are 3′ terminaldideoxynucleotide blocked P*s for comparison. In lanes 1-4 and 9-12, themutated template is used. In lanes 5-8 and 13-16, the wild-type templateis used. The PAP product and P* are indicated with their sizes. Lane Mis 120 ng of φX174-PUC19/HaeIII DNA marker. FIG. 18C: PAP with 35-merP*s: The experiment is the same as in FIG. 18B except with 35-mer P*sthat are 3′ co-terminal with the 30-mer P*s and five nucleotides longerat their 5′ termini. FIG. 18D: PAP with Vent (exo-) polymerase. Theexperiment is the same as in FIG. 18B except that Vent (exo-) was used.FIG. 18E: PAP with Pfu (exo-) polymerase. The experiment is the same asin FIG. 18B except that Pfu (exo-) was used.

FIG. 19 shows that PAP has high selectivity to detect rare mutations inthe abundance of the wild-type template. In the example of nucleotideposition 190, the mutation-specific P* matches the mutated A templatebut mismatches the wild-type T template at the 3′ terminus. Specific andefficient amplification is indicated by thick arrows. When hybridized tothe mutated A template, the P* cannot extend directly from the 3′terminal dideoxynucleotide, the 3′ terminal ddTMP must be removed bypyrophosphorolysis and the activated oligonucleotide is then extendedefficiently. Two types of nonspecific amplification from the T templateare indicated as Types I and II. The nonspecific amplification occursrarely when mismatch pyrophosphorolysis occurs to generate a wild-typeproduct that will not support efficient amplification as template forsubsequent cycles (Type I) (the error is indicated by thin arrow andestimated frequency of as low as 10⁻⁵). When both mismatchpyrophosphorolysis and misincorporation occur extremely rarely togenerate a mutated product (Type II) (the errors are indicated by thinarrows and estimated coupled frequency of 3.3×10⁻¹¹). Once the errorsoccur, the mutated product can be amplified exponentially in subsequentcycles and so it determines the selectivity.

FIGS. 20A-20B show Bi-PAP amplification. FIG. 20A: Schematic of Bi-PAPto detection a rare mutation. The mutation-specific assay with twomutated P* for nucleotide 190 is shown. The downstream and upstream P*scontain a dideoxy T and a dideoxy A at their 3′ termini, respectively.They are specific for the T:A allele at nucleotide 190 (on the right),but are mismatched to the A:T wild-type allele at their 3′ termini (onthe left). The P*s are 40 nucleotides long and overlap at their 3′termini by one nucleotide. On the left, no substantial product isgenerated from the wild-type template because of the mismatch. On theright, the mutated product is generated efficiently from the mutatedtemplate. FIG. 20B: Bi-PAP amplification directly from λ DNA. Each ofthe wild-type and mutation-specific Bi-PAP assays at nucleotide 190 wasused to amplify a 79-bp segment of the lacI gene from λ DNAs. For thewild-type assay in lanes 1-3, the two wild-type P*s have 3′ terminal ddAand ddT, respectively. For the mutation-specific assay in lanes 4-6 andlanes 7-9, the two mutated P*s are with ddT and ddA at their 3′ termini,respectively. In lanes 1, 4 and 7, 2000 copies of the wild-type templatewere added to each reaction. In lanes 2, 5 and 8, 2000 copies of themutated template were added to each reaction. In lanes 3, 6 and 9, notemplate was added. In lanes 7-9, 200 ng of human genomic DNA was addedas carrier. The product and P* are indicated. Lane M is 120 ng ofφX174-PUC19/HaeIII DNA marker.

FIGS. 21A-21C show titration of template for sensitivity and selectivityof Bi-PAP. With the mutated P*s, the wild-type template was amplified togenerate the mutated product in Experiment I. The mutated template wasamplified to generate the mutated product in Experiments II, III and IV.FIG. 21A: The mutation-specific Bi-PAP assay for A190T. In Experiment I,the copies of the wild-type λ DNA are indicated in lanes 1-5. Lane 6 isa negative control with no DNA. In Experiment II, the copies of themutated λ DNA are indicated in lane 7-11. Lane 11 (0.2 copy) is anegative control to support the dilution accuracy of copy number. Lane12 is a negative control with no DNA. In Experiment III, the copies ofthe mutated λ DNA in the presence of 2×10⁹ copies of the wild-type λ DNAare indicated in lane 13-17. Lane 18 is a negative control with only thewild-type λ DNA. In Experiment IV, the copies of the mutated λ DNA inthe presence of 100 ng of human genomic DNA are indicated in lanes19-23. Lane 24 is negative control only with the human genomic DNA. Lane“C WT” is the wild-type product control in which the wild-type P*s wereused to amplify 2000 copies of the wild-type λ DNA. Lane “C Mut” is themutated product control in which the mutated P*s were used to amplify2000 copies of the mutated λ DNA. The wild-type and mutated productswith unique mobilities are indicated. FIG. 21B: The mutation-specificBi-PAP assay for T369G. FIG. 21C: The mutation-specific Bi-PAP assay forT369C.

FIG. 22 shows a design of P* microarray for Bi-PAP resequencing. Bi-PAPcan be used for resequencing to detect unknown mutations in a knownregion on a microarray. The P*s are designed according to the wild-typetemplate. The two opposing P*s for each Bi-PAP are anchored in amicroarray spot. Each pair of arrows represents four Bi-PAPs for onenucleotide position. A mutation is indicated on the template, and itspans six overlapped P*s. On the microarray, many Bi-PAPs can beprocessed in a parallel way.

FIGS. 23A-23B show a schematic of Bi-PAP resequencing. FIG. 23A:Detection of the wild-type sequence. This is a close look at themicroarray. The P*s are designed according to the wild-type sequence. Onthe position of nucleotide A, four Bi-PAPs are synthesized with fourpairs of P*s. The four downstream P*s have identical sequence, exceptthat at the 3′ terminus either ddAMP, ddTMP, ddGMP or ddCMP, correspondsto the wild-type sequence and the three possible single basesubstitutions. The four corresponding upstream P*s have identicalsequence, except that at the 3′ terminus either ddTMP, ddAMP, ddCMP orddGMP. Each pair of P*s have one nucleotide overlap at their 3′ termini.On the next nucleotide C, another four pairs of P*s are synthesized (notshown). If the wild-type sample is added, only the wild-type Bi-PAPsgenerates the specific product that is labeled by fluorescence. In thisway, to scan a 1 kb region, you need 8000 P*s. FIG. 23B: Detection of anA to T mutation. On the mutated nucleotide T, the mutation-specificBi-PAP generates the mutated product. On the next nucleotide G, noproduct of Bi-PAP is generated because each pair of P* contains one ortwo mismatches (not shown).

FIGS. 24A-24B show Bi-PAP resequencing microarray. FIG. 24A: Detectionof the wild-type sequence. Four pairs of P*s are designed for eachnucleotide position according to the wild-type sequence. Each pair ofP*s are downstream and upstream directed, and have one overlap andcomplementary nucleotide at their 3′ termini. The wild-type P* pair arespecifically amplified on each nucleotide position. If all of thewild-type P* pairs specifically amplified, the wild-type sequence can bedetermined. FIG. 24B: Detection of the A to T mutation. With the mutatedtemplate, the mutation-specific Bi-PAP is amplified. There is a windowof no Bi-PAP signals centered by the mutation-specific Bi-PAP and threesuccessive nucleotides on each side. The paired specific subsequence issupposed to be seven nucleotides long. Any unknown single-basesubstitution can be determined, even if it is a heterozygous mutation.Also, small deletions and insertions can be detected and localized.

FIG. 25 shows PAP de novo sequencing on microarray. PAP can also be usedfor de novo DNA sequencing of an unknown region. The paired specificsubsequence is supposed to be fifteen nucleotides long. P* pairs of acomplete set of the paired specific subsequence are on a microarray withknown addresses. After the unknown DNA sample is added, Bi-PAP isperformed. All the amplified Bi-PAP products are collected and then thepaired specific subsequences of the amplified P* pairs are assembled byone-nucleotide overlapping. Thus, the unknown complementary sequence isreconstructed.

FIGS. 26A-26C show the detection of somatic mutations. FIG. 26A:Eighteen genomic DNA samples of the lacI⁺ transgenic mice were chosen. 2μg genomic DNA of each sample was amplified with the assay B to detectthe T369G mutation two times. Samples 1-10 are from livers of 25-monthold mice. Samples 11-14 are from hearts (samples 11, 13 and 14) andadipose (sample 12) of 6-month old mice. Samples 15-18 are from brainsof 10-day old mice. P=positive control that amplified the mutated λ DNA,N=negative control with no DNA, +=amplified product, −=no product. FIG.26B: The assay B was performed. In lanes 11-12, 13-16 and 17-20, 2 μg,0.5 μg and 0.125 μg of the lacI⁺ mouse genomic DNA of sample 12 wereused in each reaction, respectively. Lanes 1-10 are controls; the copynumber of the mutated λ DNA per reaction was reconstructed by two-foldserial dilutions. In lanes 1-10 and 13-20, each reaction also contained1 μg of the lacI⁻ mouse genomic DNA carrier. ss=single-stranded,ds=double-stranded. FIG. 26C: The assay B was performed. In lanes 11-14,2 μg of the lacI⁺ mouse genomic DNA of sample 3 was used in eachreaction. In lanes 15-18, 2 μg of the lacI⁺ mouse genomic DNA of sample9 was used in each reaction. Lanes 1-10 are controls; the copy number ofthe mutated λ DNA per reaction is indicated. Each control reaction alsocontained 1 μg of the lacI⁻ mouse genomic DNA carrier.

DETAILED DESCRIPTION OF THE INVENTION

The following terminology is used herein.

Pyrophosphorolysis: removal of the 3′ nucleotide from a nucleotidestrand chain by DNA polymerase in the presence of pyrophosphate (PP_(i))to generate the nucleotide triphosphate. This is the reverse of thepolymerization reaction.

PAP: Pyrophosphorolysis activated polymerization. PAP can use one P* orcan use two opposing oligonucleotides in which at least one is P*.

P*: an oligonucleotide with a non-extendible 3′ terminus (or end) thatis activatable by pyrophosphorolysis.

PAP-A: PAP-based allele-specific amplification that can be used fordetection of rare mutations (FIG. 1).

Bi-PAP-A: PAP-A performed with a pair of opposing P*, i.e.,bidirectional (FIG. 2) with at least one nucleotide overlap at their 3′termini.

PAP-R: PAP-based resequencing for detection of unknown mutations withina known sequence (FIGS. 3 and 4).

LM-PAP: ligation-mediated PAP. The nature of LM-PAP is that the templateis synthesized before PAP, such as by ligation reaction or by extensionusing terminal transferase.

LM-PCR: ligation-mediated PCR (FIG. 5).

G^(v) or A^(v) alleles: alleles of the common polymorphism of thedopamine D₁ receptor gene that was used as a model system herein (alsoreferred to herein as G⁰ or A⁰ alleles).

Linear PAP: PAP with only one P* for linear product accumulation.

Exponential PAP: PAP with two opposing oligonucleotides for exponentialproduct accumulation, and at least one is P*.

Noise rate (%): the relative yield of the mismatched product to thematched product. A specific signal for PAP is defined as a noise rate ofless than 10%.

PASA: PCR amplification of specific alleles (also known asallele-specific PCR or ARMS).

Resequencing: scanning for unknown mutations and determining the precisesequence changes within a known sequence. Resequencing is distinguishedfrom de novo sequencing.

Mutation load: the frequency and pattern of somatic mutations within atissue.

Minimal residual disease: e.g., rare remaining cancer cells in lymphnodes and other neighboring tissues or early recurrence after remission.

Non-extendible 3′ terminus (or end): a nucleotide or nucleotide analogat the 3′ terminus (or end) of oligonucleotide P* that is non-extendiblebut that is activatable by pyrophosphorolysis. Examples ofnon-extendible 3′ termini (or ends) include, but are not limited to, a2′3′-dideoxynucleotide, an acyclonucleotide, 3′-deoxyadenosine(cordycepin), 3′-azido-3′-deoxythymidine (AZT), 2′,3′-dideoxyinosine(ddI), 2′,3′-dideoxy-3′-thiacytidine (3TC) and2′,3′-didehydro-2′,3′-dideoxythymidine (d4T).

Simplex PAP: one PAP (PAP, Bi-PAP, matched or mismatched PAP, andothers) in one reaction tube or on a solid support.

Multiplex PAP: more than one PAP (PAP, Bi-PAP, matched or mismatchedPAP, and others) in one reaction tube or on a solid support, e.g.,microarray.

Matched PAP: PAP having a match between P* and its template.

Mismatched PAP: PAP having a mismatch between P* and its template.

Nested PAP: PAP using two or more pairs of P* in which one pair islocated inside a second pair on a template nucleic acid.

Hotstart PAP: PAP in which an essential reaction component is withhelduntil denaturation temperatures are approached (Charo et al., 1992;Kellogg et al., 1994; Mullis, 1991; D'Aquila et al., 1991). Essentialreaction components can be withheld by, e.g., a neutralizing antibodybound to the polymerase, sequestering a component, such as the polymersor MgCl₂ in wax, chemically modifying the polymerase to preventactivation until high temperature incubation or separating components bywax.

Truncated Amplification: an amplification method which amplifiesnon-exponentially, e.g., in a quadratic or geometric manner, with overtwo chimeric oligonucleotides and produces truncated terminal productsthat are no more than three rounds of replication from the originaltemplate. (Liu et al., 2002).

Reactive 3′ OH: is a 3′ OH that is capable of being extended by anucleic acid polymerase or ligated to an oligonucleotide.

DNA polymerases, which are critical to nucleic acid amplification,catalyze some or all of the following reactions: i) polymerization ofdeoxynucleotide triphosphates or their analogs; ii) pyrophosphorolysisof duplexed DNA in the presence of pyrophosphate (PP), [dNMP]_(n)+x[PPi]. . . [dNMP]_(n-x)+x[dNTP]; iii) 3′-5′exonuclease activity (which doesnot require PPi), and iv) 5′-3′ exonuclease activity (Duetcher andKornberg, 1969; Kornberg and Baker, 1992). For Taq and Tfl DNApolymerases, polymerization and 5′-3′ exonuclease activity have beenreported (Chien et al., 1976; Kaledin et al., 1981; Longley et al.,1990). For T7 Sequenase and Thermo Sequenase DNA polymerases,pyrophosphorolysis can lead to the degradation of specificdideoxynucleotide-terminated segments in Sanger sequencing reaction(Tabor and Richardson, 1990; Vander Horn et al., 1997).

Pyrophosphorolysis is generally of very minor significance becausePP_(i) is degraded by pyrophosphatase under normal physiologicalconditions. However, in the presence of high in vitro concentrations ofPP_(i), pyrophosphorolysis can be substantial. For oligonucleotides witha 3′ terminal dideoxy nucleotide, only pyrophosphorolysis is possible.Once the dideoxy nucleotide is removed, the activated oligonucleotidecan be extended by polymerization.

Pyrophosphorolysis activated polymerization (PAP) offers a novelapproach for retrieving a diversity of information from nucleic acids.The exceptional specificity of PAP derives from the serial coupling oftwo reactions. PAP involves the activation by pyrophosphorolysis of a 3′terminal blocked oligonucleotide (P*) followed by extension of theactivated oligonucleotide by DNA polymerization. Operationally, PAPinvolves the use of an activatable oligonucleotide (P*) in place of anormal oligonucleotide that can be directly extended. Examples of P*include an inactive dideoxy terminated oligonucleotide P* or an inactivechemically modified nucleotide lacking a 3′ hydroxyl group, such as anacyclonucleotide, or having a non-extendible nucleotide terminatedoligonucleotide P*. Acycloclonucleotides (acycloNTPs) in which the sugarring is absent are known to act as chain terminators in DNA sequencing(Sanger et al., 1977; Trainor, 1996; Gardner and Jack, 2002). Theactivation of P* is inhibited by mismatches throughout the length of theoligonucleotide. Mismatches even two nucleotides from the 5′ terminusinhibit PAP amplification.

Activation of a P* by pyrophosphorolysis offers extraordinaryspecificity throughout the length of P*. The enhanced specificity can beused to detect rare known mutations, to elucidate unknown mutations byresequencing, to determine unknown sequence by de novo sequencing, tomeasure gene expression levels, to compare two sequences, and toincrease the specificity of in vivo analysis of chromatin structure.Microarray-based programmable photochemical oligonucleotide synthesisand PAP are synergistic technologies. Thus, the enhanced specificity canbe used for rapid, microarray-based resequencing, de novo sequencing,gene expression profiling and SNP detection.

A number of methods for enzymatic nucleic acid amplification in vitrohave been developed and can be adapted to detect known sequencevariants. These include polymerase chain reaction (PCR) (Saiki et al.,1985; Saiki et al., 1988), ligase chain reaction (LCR) (Landegren, 1998;Barany, 1991) and rolling circle amplification (RCA) (Baner et al.,1998; Lizardi et al., 1998). Herein, we describe pyrophosphorolysisactivated polymerization (PAP), an approach that has the potential toenhance dramatically the specificity of PCR allele-specificamplification (Sommer et al., 1989). PAP differs from corrections withPCR in multiple ways: i) the P* oligonucleotide is blocked at the 3′terminus and must be activated by pyrophosphorolysis, ii)pyrophosphorolysis and polymerization are serially coupled for eachamplification, iii) PAP may be performed with one P* for linearamplification or with two oligonucleotides for exponentialamplification, iv) PP_(i) is necessary for the amplification, v)significant nonspecific amplification would require the serial couplingof errors of both mismatch pyrophosphorolysis and misincorporation.

The enhanced specificity of PAP relative to PASA is provided by seriallycoupling pyrophosphorolysis and polymerization. Significant nonspecificamplification requires mismatch pyrophosphorolysis and misincorporationby DNA polymerase, an extremely rare event. For example as describedherein, DNA polymerase was utilized to detect the G allele at nucleotide229 of the D₁ dopamine receptor gene. P* was synthesized either withddA, ddT, ddG or ddC at the 3′ terminus. The 3′ terminaldideoxynucleotide inhibits direct extension by polymerization, but canbe removed by pyrophosphorolysis in the presence of pyrophosphate(PP_(i)) when the P* is specifically hybridized with the complementarystrand of the G allele. The activated oligonucleotide can be extended bypolymerization in the 5′-3′ direction.

Evidence is presented that pyrophosphorolysis followed by polymerizationcan be used to increase the specificity of PASA. Significant nonspecificamplification with PAP requires the serial coupling of the two types oferrors, i.e., mismatched pyrophosphorolysis and misincorporation (FIG.1). The rate of mismatched pyrophosphorolysis is expressed as therelative rates of removal of a 3′ mismatch deoxynucleotide relative tothe correct 3′ deoxynucleotide. The rate of mismatch pyrophosphorolysisis less than 10⁻⁵ for T7 DNA polymerase (Kornberg and Baker, 1992; Wonget al., 1991). The misincorporation rate to create a substitutionmutation by polymerization, expressed as the incorporation rate of anincorrect versus a correct dNMP, was reported to be 10⁻⁵ for T7 DNApolymerase and to be 10⁻⁴ for E. coli DNA polymerase I (Kornberg andBaker, 1992; Wong et al., 1991; Bebenek et al., 1990). Similar resultswere reported for Taq DNA polymerase, 3′-5′ exonuclease-deficientmutants of T7 DNA polymerase and E. coli DNA polymerase I (Kornberg andBaker, 1992; Wong et al., 1991; Bebenek et al., 1990; Eckert and Kunkel,1990).

PAP is a method of synthesizing a desired nucleic acid strand on anucleotide acid template strand. In PAP, pyrophosphorolysis andpolymerization are serially coupled for nucleic acid amplification usingpyrophosphorolysis activatable oligonucleotides (P*). P* is anoligonucleotide that is composed of N nucleotides or their analogs andhas a non-extendible nucleotide or its analog at the 3′ terminus, suchas 3′,5′ dideoxynucleotide. When substantially hybridized on itstemplate strand, P* could not be extended directly from the 3′ terminalnucleotide or its analog by DNA polymerase, the 3′ terminal nucleotideor its analog of the P* can be removed by pyrophosphorolysis and thenthe activated oligonucleotide (<N) can be extended on the template.

The method comprises the following steps carried out serially.

(a) Annealing to the template strand a substantially complementaryactivatable oligonucleotide P*. This activatable oligonucleotide P* hasa non-extendible nucleotide or its analog at the 3′ terminus.

(b) Pyrophosphorolyzing the annealed activatable oligonucleotide P* withpyrophosphate and an enzyme that has pyrophosphorolysis activity. Thisactivates oligonucleotide P* by removal of the 3′ terminalnon-extendible nucleotide or its analog.

(c) Polymerizing by extending the activated oligonucleotide P* on thetemplate strand in the presence of nucleoside triphosphates or theiranalogs and a nucleic acid polymerase to synthesize the desired nucleicacid strand.

The PAP method can be applied to amplify a desired nucleic acid strandby the following additional steps.

(d) Separating the desired nucleic acid strand of step (c) from thetemplate strand, and

(e) Repeating steps (a)-(d) until a desired level of amplification ofthe desired nucleic acid strand is achieved.

The above PAP method can be applied to allele-specific amplification.The activatable oligonucleotide P* has one or more nucleotides that arenot complementary to the template strand. The uncomplimentarynucleotide(s) of P* may locate at the 3′ terminus of P*. The above stepof (a), (b) or (c) could not occur substantially. As the result, thedesired nucleic acid strand is synthesized substantially less.

The above PAP method can be applied with only one activatableoligonucleotide P*. (e) Repeating steps (a)-(d), a desired level ofamplification of the desired nucleic acid strand may be achievedlinearly. The targeted nucleic acid region outside the annealing regionmay be of different sizes or of different sequence contexts, so thesynthesized nucleic acid strands are of different sizes or of differentsequence contexts.

The above PAP method can be applied with two opposing oligonucleotidesof which at least one is the activatable oligonucleotide P*. Theactivatable oligonucleotide P* and the second oligonucleotide aretargeted for amplification of a nucleic acid region. Steps (a)-(c) occurto the activatable oligonucleotide P*. The second oligonucleotide issubstantially complementary to the other template strand. If the secondoligonucleotide is another activatable oligonucleotide P*, steps (a)-(c)occur. If the second oligonucleotide is a regular extendibleoligonucleotide, steps (a) and (c) occur: (modified a) annealing to itstemplate strand, followed by (modified c) polymerizing by extending theoligonucleotide on its template strand in the presence of nucleosidetriphosphates or their analogs and a nucleic acid polymerase tosynthesize the desired nucleic acid strand. (e) Repeating steps (a)-(d),or steps (a), (c) and (d), a desired level of amplification of thedesired nucleic acid strand may be achieved, e.g., exponentially. Thetargeted nucleic acid region between the two annealing regions of thetwo opposing oligonucleotides may be of different sizes or of differentsequence contexts, so the synthesized nucleic acid strands are ofdifferent sizes or of different sequence contexts.

LM-PAP involves cleavage, primer extension, linker ligation and PAP thatcan be applied for analysis of in vivo chromatin structure, such as,methylated state of chromosomes.

LM-PAP may be performed by steps (i), (ii), (iii), (iv) and (v), bysteps (i), (ii), (iii) and (vi), by steps (ii), (iii), (iv) and (v) orby steps (ii), (iii) and (vi), where the steps are as follows.

(i) The cleavage occurs chemically, enzymatically or naturally to“breakdown” nucleic acid strands. The nucleic acid usually is genomicDNA that may have lesions or nicks produced in vivo.

(ii) The primer of P1 is gene-specific and its extension includes: 1)annealing to the template strand a substantially complementary primer;2) extending the primer on the template strand in the presence ofnucleoside triphosphates or their analogs and a nucleic acid polymerase,the extension “runs off” at the cleavage site on the template strand.Steps 1) and 2) may be repeated.

The primer extension may be replaced by a P* extension (The above PAPwith only one activatable oligonucleotide P*).

(iii) The linker ligation step includes ligation of a linker to the 3′terminus of the synthesized nucleic acid strand. The linker ligationstep may be replaced by a terminal transferase extension that isnon-template dependent polymerization and an extra nucleic acid sequenceis added to the 3′ terminus of the synthesized nucleic acid strand.

(iv) PCR is performed with a second gene-specific primer (P2) togetherwith a primer specific for the linker or the added sequence by terminaltransferase.

(v) A third gene-specific P* (P3) is used to detect the PCR generatedfragments. PAP method is applied with only one activatableoligonucleotide P*. The extension of the activated oligonucleotide P*“runs off” at the end of the template strand generated in step (iv). ThePAP method may be applied in allele-specific manners. The activatableoligonucleotide P* may contain one or more nucleotides that are notcomplementary to the template strand. The uncomplimentary nucleotide(s)of P* may locate at the 3′ terminus of P*.

(vi) Instead of steps (iv) and (v), PAP method can be applied with twoopposing oligonucleotides of which at least one is the activatableoligonucleotide P*. The activatable oligonucleotide P*(P3) isgene-specific. The second oligonucleotide is specific for the linker orthe added sequence by terminal transferase. The second oligonucleotidemay be another activatable oligonucleotide P* or a regular primer. ThePAP method may be applied in allele-specific manners. The activatableoligonucleotide P* (P3) may contain one or more nucleotides that are notcomplementary to the template strand. The uncomplimentary nucleotide(s)of P* may locate at the 3′ terminus of P* (P3).

FIG. 1 shows detection of a rare mutation by allele-specific PAP(PAP-A). PAP-A can detect a rare allele with extremely high specificitybecause an allele-specific oligonucleotide with a 3′ dideoxy terminus(P*) permits the serial coupling of pyrophosphorolysis andpolymerization. For example, if an allele-specific oligonucleotide has a3′ dideoxy terminus (P*) that matches a rare “T” allele, activationoccurs by pyrophosphorolytic removal of the dideoxy nucleotide and isfollowed by polymerization (Situation A). Activation bypyrophosphorolysis does not normally occur with a mismatch at the3′terminus as with the wild-type “C” allele (Situation B). Rarely,pyrophosphorolysis does occur at a mismatch (estimated frequency 10⁻⁵),but the activated oligonucleotide is extended to produce wild-typesequence (Situation C). A product that supports efficient amplificationis generated when mismatch pyrophosphorolysis occurs, a polymerase errorthat inserts A opposite C in template DNA (Situation D). The frequencyof mismatch pyrophosphorolysis coupled with the polymerase mutation isestimated at 10⁵×3×10⁻⁶=3×10⁻¹¹.

PAP has a potential specificity of 3×10⁻¹¹. Approaching this potentialrequires a design that eliminates confounding sources of error. Forexample, extension errors from non-blocked upstream oligonucleotides cangenerate a product with the mutation of interest. If themisincorporation rate for TaqFS is about 10⁻⁵ per nucleotide and onlyone of the three misincorporations generates the mutation of interest,the error rate is about 3.3×10⁻⁶. Polymerases that contain aproofreading function might have an error rate per specific mutation of3×10⁻⁷. Polymerases or polymerase complexes with lower error rates wouldimprove specificity further.

One approach utilizes linear PAP. Linear PAP-A may be performed for 40cycles with only P* in the presence of a fluorescent or radiolabeledddNTP. A labeled terminated product of defined size will be generatedwhen P* is activated. Linear PAP-A has the advantage of utilizing onlythe original genomic DNA and eliminating error due to misincorporationfrom extension of an unblocked upstream primer. However, the sensitivityof detection is limited because the level of amplification is notgreater than the number of cycles. For a simple genome like lambdaphage, a detection specificity of 10⁻⁶ is possible. The specificity oflinear PAP-A depends critically on the absence of unblocked, extendibleoligonucleotides. To achieve a robust specificity of 10⁻⁶, unblockedextendible oligonucleotides should be present at 10⁻⁷. This may beachieved by treating gel purified P* (about 99.99% pure with our presentprotocol) with a 3′ to 5′ exonuclease to degrade unblocked moleculesfollowed by repurification by gel electrophoresis.

A second approach is bidirectional PAP-A (Bi-PAP-A; FIG. 2). InBi-PAP-A, both the downstream and upstream oligonucleotides are P*s thatare specific for the nucleotide of interest. The P*s overlap at their 3′termini by one nucleotide. This design eliminates extension error from anon-blocked upstream oligonucleotide. This design should not be limitedby small amounts of active contaminating oligonucleotide to which thedideoxy terminus has not been added (about 0.01% with our currentprotocol) because the product generated will be that of a control andwill not be a substrate for efficient amplification in subsequentcycles.

Bi-PAP-A generates a product that is the size of a primer dimer.However, it is not a primer dimer in the conventional sense, in thattemplate DNA with a mutation of interest is an intermediate required togenerate a product that is an efficient substrate for amplification insubsequent cycles. Bidirectional PAP-A eliminates important bottlenecksto specificity and has the potential to reach a specificity of 10⁻⁹.

As shown in FIG. 2, both the downstream and the upstream P*s arespecific for the nucleotide of interest at the 3′ termini (an A:T basepair in this example). In the initial round of amplification fromgenomic DNA, segments of undefined size will be generated. In subsequentrounds, a segment equal to the combined lengths of the oligonucleotideminus one will be amplified exponentially. Nonspecific amplificationoccurs at lower frequencies because this design eliminatesmisincorporation error from an unblocked upstream oligonucleotide thatcan generate the A:T template from a G:C wild-type template with anerror rate of 3×10⁻⁶. The P*s may be 30-60 nucleotides for mostefficient amplification. Situation A shows that a template with a rareA:T allele will be amplified efficiently. Both the upstream and thedownstream P*s are amplified efficiently. Situation B shows that if theDNA template contains the wild-type G:C sequence, neither the downstreamnor the upstream P* will be activated substantially.

Rapid resequencing will facilitate elucidation of genes that predisposeto cancer and other complex diseases. The specificity of PAP lendsitself to resequencing. P*s may be photochemically synthesized onmicroarrays using flexible digital micromirror arrays.

Microarrays of immobilized DNA or oligonucleotides can be fabricatedeither by in situ light-directed combinational synthesis or byconventional synthesis (reviewed by Ramsay, 1998; Marshall and Hodgson,1998). Massively parallel analysis can be performed. Photochemicalsynthesis of oligonucleotides is a powerful means for combinatorialparallel synthesis of addressable oligonucleotide microarrays(Singh-Gasson et al., 1999; LeProust et al., 2000). This flexiblealternative to a large number of photolithographic masks for each chiputilizes a maskless array synthesizer with virtual masks generated on acomputer. These virtual masks are relayed to a digital micromirrorarray. An ultraviolet image of the virtual mask is produced on theactive surface of the glass substrate by a 1:1 reflective imagingsystem. The glass substrate is mounted in a flow cell reaction chamberconnected to a DNA synthesizer. Cycles of programmed chemical couplingoccur after light exposure. By repeating the procedure with additionalvirtual masks, it is possible to synthesize oligonucleotide microarrayswith any desired sequence. The prototype developed by Singh-Gasson, etal. synthesized oligonucleotide microarrays containing more than 76,000features measuring 16 square microns.

By combining programmable photochemical oligonucleotide synthesis withdigital mirrors and oligonucleotide extension of P*, a high throughputand automated method of resequencing is possible. PAP-R may detectvirtually 100% of single base substitutions and other small sequencevariants because of its high redundancy; the mismatch spanned by theseveral overlapping P* oligonucleotides will prevent activation of acluster of overlapping P*s. One strategy for resequencing is shown inFIGS. 3 and 4. FIG. 3 shows a schematic of PAP-R performed on amicroarray with programmable photochemical oligonucleotide: PAP can beused for resequencing to detect unknown mutations. On this microarray,the wild-type template is indicated. The P*s are designed according tothe wild-type template. The P*s that overlap with the mutation generatelittle or no signal indicated as “Low” PAP signal.

FIG. 4 shows an example of solid support-based, e.g., microarray-based,resequencing to detect a G to A mutation. Linear PAP is performed withfour different dye-labeled ddNTPs as substrates for single-baseextensions. P*s have a specific region of 16 nucleotides within the 3′region of the oligonucleotide. Homozygous or hemizygous DNA template isutilized in the example. Sets of four P*s, with identical sequenceexcept for the four ddNMPs at the 3′ terminus, are synthesized for eachnucleotide position on the sense strand of the wild-type sequence. TheP* with a ddA at the 3′ terminus generates a PAP signal at the site ofthe G-A mutation. The mutation also creates a 15 base “gap” of no PAPsignal for the subsequent overlapping 15 sets of P*s. For heterozygousmutation, the P*s with ddA and ddG provide PAP signals. The heterozygousmutation also generates the 15-base “gap” of 50% signal intensity (whichis flanked by signals of 100% intensity). For added redundancy withheterozygotes samples, antisense P*s can be utilized (not shown). Anunknown single-base substitution can be determined by combination of thetwo sets of P*s. Small deletions and insertions can be detected andlocalized.

With 100,000 oligonucleotides per microarray, about 12 kb can beresequenced from downstream and upstream directions. The detection ofvirtually all mutations requires supplementation of the standard Geniom®instrument software. For wild-type sequence, the signal intensities mayvary. Certain oligonucleotides will generate a weaker signal due tosecondary structure and other factors. The pattern of signal fromwild-type samples should be distinguished reliably from the patterngenerated by a given sequence change. The preliminary data suggest thatalmost all mismatches will inhibit activation dramatically. Because ofthe redundancy, mutations may be reliably distinguished from thewild-type even if a significant minority of single base mismatches doesnot inhibit activation substantially.

It is becoming increasingly apparent that in vivo chromatin structure iscrucial for mammalian gene regulation and development. Stable changes inchromatin structure often involve changes in methylation and/or changesin histone acetylation. Somatically heritable changes in chromatinstructure are commonly called epigenetic changes (Russo and Riggs, 1996)and it is now clear that epigenetic “mistakes” or epimutations arefrequently an important contributing factor to the development of cancer(Jones and Laird, 1999).

One of the few methods for assaying in vivo chromatin structure, and theonly method with resolution at the single nucleotide level, isligation-mediated PCR (LM-PCR) (Mueller and Wold, 1989; Pfeifer et al.,1989). LM-PCR has been used to assess chromatin structure, methylationand damaged DNA. FIG. 5 shows a schematic of LM-PCR in which a DNAlesion in the starting DNA is indicated by a small diamond. LM-PCRinvolves cleavage, primer extension, linker ligation and PCRamplification. LM-PAP is similar to LM-PCR except that activatableoligonucleotide P*s are used.

LM-PCR has proven to be an important technique, now having been used inover 100 published studies (Pfeifer et al., 1999). Many aspects ofchromatin structure can be determined by LM-PCR, such as the location ofmethylated cytosine residues, bound transcription factors, or positionednucleosomes. Importantly, the structure is determined in cells that areintact and have been minimally perturbed. UV photo-footprinting, forexample, is performed by UV irradiating tissue culture cells in a Petridish, immediately extracting the DNA, and performing LM-PCR to determinethe location of thymidine dimers, the formation of which is affected bybound transcription factors.

Allele-specific LM-PAP can be applied to quantitatively determine thelevel of in vivo methylation. The background of LM-PCR currently limitsreliable estimation of the level of methylation. It is generallyconsidered that 0%, 50% and 100% methylation can be determined, butdistinguishing finer gradations is not reliable. With a marked reductionin background in LM-PAP, 0%, 20%, 40%, 60%, 80%, and 100% methylationstandards may be distinguished reliably. It will be of particularinterest to utilize allele-specific LM-PAP to examine the level ofmethylation in imprinted regions, or in active versus inactiveX-chromosomal genes in females. It is anticipated that LM-PAP willdecrease the skill and experience needed to examine chromatin structure,thereby facilitating analysis of chromatin structure by morelaboratories.

LM-PAP has a diversity of applications. It will be of particularinterest to utilize allele-specific PAP to examine differentialmethylation and chromatin structure in imprinted genes or in activeversus inactive X chromosomal genes in females. In addition, therelationship between mutagens, DNA damage, and mutagenesis can beexamined.

In PAP, as described above and illustrated herein, pyrophosphorolysisand polymerization by DNA polymerase are coupled serially by usingpyrophosphorolysis activatable oligonucleotide. In PAP sequencing, theprinciple is based on the specificity of PAP and in turn on the basepairing specificity of the 3′ specific subsequence. This property of the3′ specific subsequence can be applied to scan for unknown sequencevariants, to determine de novo DNA sequence, to compare two DNAsequences and to monitor gene expression profiling.

PAP is highly sensitive to mismatches along the length of P* in PAP withone P* and one opposing unclocked oligonucleotide. The specificity ofPAP is also affected by P* length and mismatch. If the allele-specificnucleotide of P* is at the 3′ terminus, only the specific allele isamplified and the specificity is not associated with P* length. If theallele-specific nucleotide is not at the 3′ terminus of P*, thespecificity is associated with P* length. 26 mer P* has a 3′ specificsubsequence of three-nucleotides within this region any mismatch inhibitthe amplification. 18-mer has a 3′ specific subsequence of 16nucleotides.

Bi-PAP is a form of PAP. In Bi-PAP with two opposing P*s, each P* hasits own 3′ subsequence, i.e., within this region any mismatch inhibitthe amplification of Bi-PAP. For example, when the allele-specificnucleotide of the P* pair is at their 3′ termini, only the specificallele was amplified, no matter what the lengths of the P*s are 40, 35or 30 nucleotides. The length of the paired specific subsequence isaddition of the P* pair minus one.

The length of the paired specific subsequence may be affected by thesequence context and size of each P*, the type of the 3′ terminalnon-extendible nucleotide, the template sequence, the DNA polymerase,other components like ions, and cycling conditions. When the templatecontains repeated sequences or homogenous polymer runs longer than thelength of the P* pair, P* may lose specificity for anchoring.

Resequencing is the sequencing of a known region to detect unknownmutations. The property of the paired specific subsequence of Bi-PAP canbe applied to scanning for unknown sequence variants or re-sequencing ofpredetermined sequences in a parallel way.

A Bi-PAP resequencing is shown in FIGS. 22, 23A, 23B, 24A and 24B.Briefly, the wild-type sequence can be determined, and any single basesubstitution can be determined with the type and position. An unknownsmall deletion and insertion can be detected and localized. In order toidentify a specific type of deletion or insertion, it is possible to addcorresponding Bi-PAPs. For fingerprinting, which can provide informationregarding mutation position, fewer numbers of Bi-PAPs can be used.

The concept of Bi-PAP de novo DNA sequencing makes use of the completeset of paired specific subsequence of the P* pair to identify thepresence of the paired specific subsequence in the de novo sequence.

Bi-PAP de novo DNA sequencing on microarray is shown in FIG. 25.Briefly, the procedure first collects all the Bi-PAP amplifications withtheir P* pairs and then reconstructs the unknown DNA sequence from thiscollection by ordering the paired specific subsequences.

For comparison of two DNA sequences to see if they are the same ordifferent, there is a simple way to reduce the number of P* pairs byusing an incomplete set of the specific subsequences of the P* pair. Byarranging them in a particular order, it is possible to identify thechromosomal locations as well as the sequences.

To monitor gene expression profiling, where up to 6×10⁴ to 10⁵transcripts are expressed and details of the precise sequence areunnecessary, Bi-PAP can be applied. A set of P* pairs which canspecifically amplify unique motifs in genes can be designed for Bi-PAP.

This property of the base pairing specificity of Bi-PAP can be appliedto scan for unknown sequence variants, to determine de novo DNAsequence, to compare two DNA sequences and to monitor gene expressionprofiling. A Bi-PAP array is possible. Each pair of two opposing P*s canbe immobilized at an individual spot on a solid support, e.g.,microarray, thus allowing all the Bi-PAP reactions to be processed inparallel.

For PAP, the activatable oligonucleotide has a non-extendible 3′terminus that is activatable by pyrophosphorolysis (hereinafter referredto as a non-extendible 3′ terminus). Any 3′ terminal non-extendibleoligonucleotide can be used, if it can hybridize with the templatestrand, the 3′ terminal nucleotide can be removed by pyrophosphorolysis,and the activated oligonucleotide can be extended. Examples ofnon-extendible 3′ terminus include, but are not limited to, anon-extendible 3′ deoxynucleotide, such as a dideoxynucleotide, or achemically modified nucleotide lacking the 3′ hydroxyl group, such as anacyclonucleotide. Acyclonucleotides substitute a 2-hydroxyethoxymethylgroup for the 2′-deoxyribofuranosyl sugar normally present in dNMPs.

Alternative blocking agents may increase the selectivity ofpyrophosphoroloysis for a complete match, thereby further enhancing theselectivity of PAP for detecting rare mutations. Finally, alternativeblocking agents may be less expensive or more readily automatable,thereby improving the cost-effectiveness of PAP and facilitating PAPmicroarray-based resequencing.

In addition, P*s not blocked with dideoxynucleotides extends theselection of DNA polymerases which can be used for PAP. As demonstratedherein, Family I polymerases may be used for PAP when the 3′ terminalnon-extendible oligonucleotide contains a dideoxynucleotide or anacyclonucleotide. Family II polymerases may be used for PAP when the 3′terminal non-extendible oligonucleotide contains an acyclonucleotide.

EXAMPLES

The invention can be understood from the following Examples, whichillustrate that PAP can be used to identify a known mutation in apolymorphic site within the human D₁ dopamine receptor gene. The effectsof the dideoxyoligonucleotide sequences, acyclonucleotide sequences, DNApolymerases, PP_(i) concentrations, allele-specific templates, pH, anddNTP concentrations were examined. The experiments reported in theExamples were conducted for proof of principle. The following examplesare offered by way of illustration and are not intended to limit theinvention in any manner. Standard techniques well known in the art orthe techniques specifically described therein were utilized.

Example 1 Preparation of Template by PCR

A 640-bp region of the human D₁ dopamine receptor gene was amplified byPCR with two primers (T=5′ GAC CTG CAG CAA GGG AGT CAG AAG 3′ (SEQ IDNO:1) and U=5′ TCA TAC CGG AAA GGG CTG GAG ATA 3′ (SEQ ID NO:2)) (FIG.6A). The TU:UT duplexed product spans nucleotides 33 to 672 in GenBankX55760 and the G+C content is 55.3%. A common A to G polymorphism islocated at nucleotide 229, resulting in three genotypes of G/G, A/A andG/A (Liu et al., 1995). The PCR mixture contains a volume of 50 μl: 50mM KCl, 10 mM Tris/HCl, pH 8.3, 1.5 mM MgCl₂, 200 μM each of the fourdNTPs (Boehringer Mannheim), 0.1 μM of each primer, 2% DMSO, 1 U of TaqDNA polymerase (Boehringer Mannheim) and 250 ng of genomic DNA from G/Ghomozygote, A/A homozygote or G/A heterozygotes. Cycling conditionsincluded: denaturation at 95° C. for 15 seconds, annealing at 55° C. for30 seconds, and elongation at 72° C. for one minute, for a total of 35cycles (Perkin-Elmer GeneAmp PCR system 9600). The PCR product waspurified from primers and other small molecules by approximately10,000-fold by three times of retention on a Centricon® 100microconcentrator (Amicon). The amount of recovered PCR product wasdetermined by UV absorbance at 260 nm.

Synthesis of P* by Adding a 3′-Dideoxynucleotide

The deoxynucleotide oligonucleotide was synthesized by PerseptiveBiosystems 8909 Synthesizer (Framinsham) and purified by oligopurecartridges (Hamilton) in the City of Hope DNA/RNA Chemistry Laboratory.The 3′ terminal dideoxynucleotide was added by terminal transferase. Themixture contained a total volume of 40 μl: 200 mM potassium cacodylate,25 mM Tris/HCl (pH 6.6 at 25° C.), 2.5 mM CoCl₂, 0.25 mg/ml of BSA, 4000pM of the oligonucleotide, 2.5 mM 2′,3′-ddNTP (the molar ratio of the3′-OH terminus to ddNTP was 1:25) (Boehringer Mannheim), 125 U ofterminal transferase (Boehringer Mannheim). The reaction was incubatedat 37° C. for 1 hour and then stopped by adding EDTA at 5 mM finalconcentration. After desalting by using butanol, thedideoxyoligonucleotide was purified by preparative 7M urea/20%polyacrylamide gel electrophoresis in TBE buffer (90 mM Tris/borate, 1mM EDTA, pH 8.3) (Maniatis et al., 1982). The amount of the recovered P*was determined by UV absorbance at 260 nm.

Since small amounts of unterminated oligonucleotide would result innon-specificity of pyrophosphorolysis, each dideoxyoligonucleotide was³²P-labeled at the 5′ terminus by T4 polynucleotide kinase and then waselectrophoresed through a 7M urea/20% polyacrylamide gel. Only P*products were visible even when the gel was overexposed (data notshown). It is estimated that more than 99.99% of P* contained adideoxynucleotide at the 3′ terminus.

Pyrophosphorolysis Activated Polymerization

A 469-bp region within the TU:UT duplexed template was amplified by PAPwith oligonucleotides P* and U, or with only one P* (Table 1 and FIG.6A). The PU:UP duplexed product corresponds to nucleotides 204 to 672 inGenBank X55760 and the G+C content is 55.6%. Unless stated, the PAPreaction mixture contained a total volume of 25 μl for Tfl DNApolymerase: 75 mM KCl, 20 mM Tris/HCl (pH 7.4), 1.5 mM MgCl₂, 40 μM eachof the four DNTPs (dATP, dTTP, dGTP and dCTP), 0.2 μM P*, 0.05 μM Uoligonucleotide, 300 μM Na₄PP_(i) (the 20 mM stock solution was adjustedby HCl to pH 8.0), 1 μCi of [α-³²P]-dCTP (3000 Ci/nmole, Amersham), 1 Uof Tfl DNA polymerase (Promega) and 2 ng of TU:UT. For Taq DNApolymerase, the reaction mixture was the same except for 50 mM KCl, 10mM Tris/HCl (pH 7.4), 2.0 mM MgCl₂ and 1 U of Taq DNA polymerase(Boehringer Mannheim). The mixtures of PCR and other controls were thesame except for the primers added. Cycling conditions included: 94° C.for 15 seconds, 55° C. for one minute, ramping to 72° C. for one minuteand 72° C. for two minutes, for a total of 15 cycles.

TABLE 1 Oligonucleotides used in PAP Tem-                                    G plate 5′. . . AATCTGACTGACCCCTATTCCCTGCTT GGAAC . . . 3′ (SEQ ID NO: 3)                                    A NameOligonucleotide sequence 5′-3′ (SEQ ID NO:) Purpose D₁            ACTGACCCCTATTCCCTGCTT^(b )(4) Control D₁G*^(a)           ACTGACCCCTATTCCCTGCTTG*^(b )(5) 3′ddG and G allele specificity co-localized D₂G*           ACTGACCCCTATTCCCTGCTTGG* (6) G allele specificity 5′ to ddGD₃G*            ACTGACCCCTATTCCCTGCTTGGG* (7) G allele specificity 5′to ddG D₄G*            ACTGACCCCTATTCCCTGCTTGGGG* (8) 3′ddG mismatches template D₅G*        TCTGACTGACCCCTATTCCCTGCTTG* (9)D₁G*, with 5′ extended bases D₆A*         TGACTGACCCCTATTCCCTGCTTA* (10) 3′ ddA and A allele-specificityco-localized U TCATACCGGAAAGGGCTGGAGATA (11) Upstream oligonucleotideAllele-specific 3′ terminal nucleotide^(d) nucleotide^(c) From 3′ SizeT_(m) Amplification^(f) Name Type Match Type terminus (bp) (base) (°C.)^(c) G allele A allele D₁ dT Yes — +1 21 64 Yes Yes D₁G* ddG Yes G 022 68 No No D₂G* ddG Yes G −1 23 72 No No D₃G* ddG Yes G −2 24 76 Yes NoD₄G* ddG No G −3 25 80 No No D₅A* ddG Yes G 0 26 80 Yes No D₆A* ddA YesA 0 24 72 No No U dA Yes — — 24 72 Yes Yes ^(a)D₁G* was produced byadding a G dideoxynucleotide to the 3′ terminus of the D₁,* = adideoxynucleotide at the 3′ termninus. ^(b)The T means the 3′ terminusis T deoxynucleotide and G* means the 3′ termninus is Gdideoxynucleotide. The bold capital G and A are the G and A basescorresponding to G and A alleles, respectively. The first base at the 5′terminus corresponds to nucleotide 208 in GenBank X55760. ^(c)The 3′terminal base is a deoxynucleotide or dideoxynucleotide, and creates amatch (Yes) or a mismatch (No) with the corresponding base on thecomplementary strand of the template. ^(d)The allele-specific nucleotideis G or A and its distance to the 3′ terminus is assigned: 0 = at the 3′terminus, +1 = one base downstream from the 3′ terminus, −1 = one baseupstream from the 3′ terminus, −2 = two bases upstream from the 3′terminus, and −3 = three bases upstream from the 3′ terminus. ^(e)TheT_(m) for oligonucleotides was estimated to be 4° C. X (G + C) + 2° C. X(T + A) at 1 M NaCl (Miyada and Wallace, 1987). ^(f)The amplificationwith U and one P* or with only one P*.

The reaction was electrophoresed through a standard 2% agarose gel. Thegel was stained with ethidium bromide for UV photography by a CCD camera(Bio-Rad Gel Doc 1000), dried and subjected to Kodak X-OMAT™ AR film forautoradiography.

Restriction Digestion

Each of the three restriction endonucleases of AciI(5′C▾CGC3′/3′GGCA▴G5′) EaeI (5′Py▾GGCCPu3′/3′PuCCGG▴Py5′) and Eco0109I(5′PuG▾GNCCPy3′/3′PyCCNG▴GPu5′) has a restriction site within the PU:UPduplex. The G/G alleles were amplified by PAP with D₅G* and U; PCRamplification with D₁ and U was used as the control. 40 μl of the PAPreaction and 2 μl of the PCR reaction were purified and concentratedwith a Centricon® 100 microconcentrator, and the products digested bythe restriction endonuclease: 2.5 U of AciI in 1×NE buffer 3; or 3 U ofEaeI in 1×NE buffer 1; or 30 U of Eco0109I in NE buffer 4 with BSA (allof the above enzymes and buffers from New England BioLabs). 10 μl of thereaction was incubated at 37° C. for 2 hours. The digestion reaction waselectrophoresed through a standard 2% agarose gel as described above.

Principle of PAP

Tfl and Taq DNA polymerases were shown to contain pyrophosphorolysisactivity. Tfl DNA polymerase was utilized to detect the G allele atnucleotide 229 of the D₁ dopamine receptor gene (Liu et al., 1995) (FIG.6A). P* was synthesized with either ddG or ddA at the 3′terminus (seeTable 1). The 3′terminal dideoxynucleotide inhibits direct extension bypolymerization, but can be removed by pyrophosphorolysis in the presenceof pyrophosphate (PP_(i)) when the P* is specifically hybridized withthe complementary strand of the G allele. The degraded oligonucleotidecan be extended by polymerization in 5′-3′direction (FIGS. 6B and 6C).

The enhanced specificity of PAP relative to PASA is provided by seriallycoupling pyrophosphorolysis and polymerization. Significant nonspecificamplification requires mismatch pyrophosphorolysis and misincorporationby DNA polymerase, an extremely rare event (FIG. 7).

Specific Amplification with D₅G* and D₃G*

PAP was performed with two oligonucleotides (P* and U), Tfl DNApolymerase and DNA template of the G/G and A/A alleles. Multiple P* weretested (Table 1). D₅G* (the allele-specific nucleotide anddideoxynucleotide are co-localized to the 3′ terminus and D₃G* (theallele-specific nucleotide is two bases from the 3′ terminus)specifically amplified the G allele in the presence of PP_(i) (FIG. 8A).Without added PP_(i), no specific product was observed with D₅G*,indicating that added PP_(i) was an essential component for PAP (FIG.8B, lanes 6 and 15). Faint products with D₃G* in lane 4 and with D₄G* inlane 5 were observed (FIG. 8B) (see below).

Effects of pH, [PP_(i)] and [dNTP] and Enzyme

Each of the above parameters was examined. PAP was most efficient at pHbetween 7.4 and 7.7, at [PP_(i)] between 200 μM and 400 μM, and at[dNTPs] between 25 μM and 50 μM (Table 2). Taq DNA polymerase cansubstitute for Tfl with similar efficiencies (Table 2).

TABLE 2 Parameters affecting PAP PAP efficiency^(b) Parameter D₅G*-UD₃G*-U pH^(a) 8.1 − − 7.9 − − 7.7 ++ +++ 7.5 ++ +++ 7.4 ++ +++ 7.15 + +PP_(i) ^(a) 1000 − − (μM) 800 − ± 600 − ++ 400 ++ +++ 200 ++ +++ 0 − ±All dNTPs 200 − ± changed^(a) 100 − ± (μM) 50 ++ +++ 25 ++ ++++ dGTP 100± ++ changed^(a,c) 50 ± ++ 25 ± ++ dATP 100 − + changed^(a,c) 50 − + 25− ++ Taq DNA G allele and PP_(i) ++ +++ polymerase A allele and PP_(i) −− G allele and no PP_(i) − ± ^(a)Tfl DNA polymerase was used to amplifythe G/G alleles under the conditions in Materials and Methods, exceptfor the factors indicated ^(b)The PAP efficiency is indicated as: −, nospecific product(s); ±, very weak specific product(s); +, weak specificproduct(s); ++, moderate specific product(s); +++, strong specificproduct(s); ++++, very strong specific product(s). ^(c)The indicatedconcentration was changed but the others were kept at 200 μM.

Identity of Specific Products

In order to confirm the identity of the specific products, restrictionendonuclease digestion was performed (FIG. 9). Each of the threerestriction endonucleases of AciI, EaeI and Eco0109 has a restrictionsite with the PU:UP duplex. The expected restriction fragments werefound. Similar results were observed with D₃G* and U.

The specific products of PAP with D₅G* and U revealed two specific bandson the agarose gel, i.e., PU:UP and UP; because U was more efficientthan D₅G*, under our amplification conditions. In order to confirm this,the G/G alleles were amplified by PAP using Tfl DNA polymerase with D₅G*and U as previously. The products were denatured and electrophoresedthrough a denaturing polyacrylamide gel. Only one specific band insingle-stranded form was observed, indicating that the specific PAPproducts contain the duplexed and single stranded segments. The sameresult was observed with D₃G* and U.

Linear PAP

PAP was performed for linear amplification with only one P* from the G/Gand A/A alleles in the presence of PP_(i). The specific products of PAPwere obtained with D₃G* and with D₅G*, but not with the other P* (FIG.10, lanes 4 and 6). The efficiency of P* was affected by theoligonucleotide size, the 3′-terminal dideoxynucleotide and the positionof the allele-specific nucleotide.

FIGS. 6A-6C show schematic of PAP. FIG. 6A. A duplexed DNA templateTU:UT is amplified with two oligonucleotides P* and U, Tfl DNApolymerase, dNTPs, pyrophosphate and [α-³²P]-dCTP. P*=pyrophosphorolysisactivatable oligonucleotide. In this example P* is D₅G* and TU:UT is a640-bp segment of the dopamine D₁ receptor gene. FIG. 6B. D₅G* has a Gdideoxynucleotide at the 3′ terminus, and it is specific to thecomplementary strand of the G allele, but mismatches the A allele at the3′ terminus (Table 1). Removal of the dideoxy G by pyrophosphorolysis isfollowed by polymerization for each amplification. FIG. 6C.Autoradiogram of PAP from the G/G, A/A and G/A genotypes. When the Gallele is present, the radioactively labeled specific products of 469bases (duplex PU:UP and excess antisense strand UP) are produced, sincethe low rate of pyrophosphorolysis by Tfl polymerase implies thatoligonucleotide U has a much higher efficiency than oligonucleotide P*.Electrophoresis for a longer period separates PU:UP from UP. Otherproducts of UT and UT:TU are indicated. Note that TU:UT derives fromannealing of excess radioactively labeled UT with non-radioactivelylabeled TU original template. PAP was also performed with D₃G* and Ufrom the G/G, A/A and G/A genotypes, and similar results were obtained.

FIGS. 7A-7B show enhanced specificity of PAP with D₅G*. The specificityof PAP is compared with that of PASA to exponentially amplify a templatepool of G and A alleles. FIG. 7A. The specific amplification of PASAderives from the high efficiency of primer extension when the primermatches the G allele. The nonspecific amplification results frommismatch extension from the A allele. When this occurs, it results in anefficiency substrate for further amplification. The thickness andposition of the arrow represent the amplification efficiency in eachcycle. FIG. 7B. The specific amplification of PAP from the G alleleoccurs at high efficiency. Two types of nonspecific amplificationsoriginate from the A allele: (i) nonspecific amplification can occur atlow efficiency by mismatch pyrophosphorolysis resulting in a A:Thomo-duplex PU:UP product, which is not an efficient template forsubsequent amplification; (ii) nonspecific amplification can occur atextremely low efficiency by both mismatch pyrophosphorolysis andmisincorporation to produce a G:T hetero-duplex PU:UP product, but onceit occurs, it provides an efficiency template for subsequentamplification. A similar tendency of nonspecific amplifications issuggested for linear amplification by PAP with only D₅G*. It should benoted that allele-specific nucleotide of P*, such as D₃G*, may be nearbut not at the 3′ terminus. In that case nonspecific amplification ofPAP requires both mismatch pyrophosphorolysis and mismatch extension.While both variations of PAP should have higher specificity than PASA,the highest specificity is predicted when the 3′ terminal dideoxynucleotide is also the allele-specific nucleotide.

FIGS. 8A-8B show specific amplification with D₅G* and D₃G*. PAP wasperformed in the presence (FIG. 8A) or absence (FIG. 8B) of added PP_(i)with two oligonucleotides for exponential amplification. Theoligonucleotides are listed in Table 1. Extension controls with only Uidentify the positions of TU:UT and UT. Extension controls with D₁identify the position of PU. PCR controls of D₁ and U identify thepositions of PU:UP and PU:UT. Only 20% of the extension reaction with D₁and the PCR reaction were loaded relative to other lanes.

FIG. 9 shows restriction endonuclease digestion. To show specificity ofPAP, samples from the experiment shown in FIG. 8 were digested withAciI, EaeI and Eco0109I restriction endonucleases. Each enzyme has arestriction site within PU:UP. PAP amplified the G/G alleles with D₅G*and U, and 5% of PCR reaction with D₁ and U were taken as control. AciIproduces a 236 bp and a 233 bp fragments from PU:UP and a 407 bp and a233 bp fragments from TU:UT. EaeI produces a 289 bp and a 180 bpfragments from PU:UP and a 460 bp and a 180 bp fragments from TU:UT.Eco0109I produces a 348 bp and a 121 bp fragments from PU:UP and a 107bp, a 412 bp and a 121 bp fragments from TU:UT. The arrows indicate thedigestion products expected from PU:UP.

FIG. 10 shows linear PAP. PAP was performed with only one P* in thepresence of added PP_(i). 20% of the reaction with D₁ was loadedrelative to other lanes (lanes 1 and 10). No=no oligonucleotide added.

Enhanced Specificity of PAP with D₅G*

Example 1 provides evidence that pyrophosphorolysis followed bypolymerization may be used to increase the specificity of PASA.Significant nonspecific amplification requires the serial coupling ofthe two types of errors (FIG. 7). The mismatch pyrophosphorolysis rateto remove a mismatch deoxynucleotide at the 3′ terminus, expressed asthe removal rate of an incorrect versus a correct dNMP, was reported atless than 10⁻⁵ for T7 DNA polymerase (Kornberg and Baker, 1992; Wong etal., 1991). The misincorporation rate to create a substitution mutationby polymerization, expressed as the incorporation rate of an incorrectversus a correct dNMP, was reported as to be 10⁻⁵ for T7 DNA polymeraseand to be 10⁻⁴ for E. coli DNA polymerase I (Kornberg and Baker, 1992;Wong et al., 1991; Bebenek et al., 1990). Similar results were reportedfor Taq DNA polymerase and for 3′-5′ exonuclease-deficient mutants of T7DNA polymerase and E. coli DNA polymerase I (Kornberg and Baker, 1992;Wong et al., 1991; Eckert and Kunkel, 1990). The specificity due to the(i) nonspecific amplification in PAP with D₅G* is estimated to be 10⁻⁵per cycle, if the mismatch pyrophosphorolysis rate of a ddNMP is thesame as dNMP. The specificity due to the (ii) nonspecific amplificationis estimated to be 3.3×10⁻¹¹, if the mismatch pyrophosphorolysis and themisincorporation are serially coupled.

Essential Components of PAP

Each P* was tested by utilizing Tfl or Taq DNA polymerases to amplifythe G/G and A/A alleles. The specific amplification requires thepresence of PP_(i) and allele-specific template. In addition, theamplification efficiency is affected by the oligonucleotide size, the 3′terminal dideoxynucleotide, the position of the allele-specificnucleotide relative to the 3′ terminus of P*.

It is not clear why D₁G* and D₂G* did not generate the specific signals,but it may be related to a threshold stability of duplex between P* andthe template. D₆A*, which contains A dideoxynucleotide at the 3′terminus, did not generate the specific signal, which may be associatedwith different incorporation efficiencies of ddNTPs by polymerization.Klenow fragment of E. coli DNA polymerase I, Taq DNA polymerase and ΔTaqDNA polymerase incorporate ddGTP more efficiently than other ddNTPs(Sanger et al., 1977; Tabor and Richardson, 1995; Vander Horn et al.,1997). The rate of ddNTP incorporation also varies depending on thetemplate sequence and can be 10-fold higher at some bases relative toothers (Sanger et al., 1977). Another possibility is that D₆A* isshorter in size with a lower T_(m).

In PAP without added PP_(i), very faint false signals were generatedwith D₃G* and with D₄G* (FIG. 8B). One possibility is thatoligonucleotide dimers can form and trigger nonspecificpyrophosphorolysis of P* in later cycles after “endo-” PP_(i) isreleased from the by-polymerization to generate UT. 3′terminal degradedD₃G* and D₄G* can be hybridized and extended as false signal.Oligonucleotide dimers were observed with D₃G* and D₄G*. Anotherpossibility with D₃G* is that the specific pyrophosphorolysis can occurin later cycles after “endo-” PP_(i) is released. A third possibility isthat D₃G* and D₄G* were contaminated by minimal D₃ and D₄ which were notfully added by G dideoxynucleotide at 3′ termini.

Comparison with Other Technologies

A number of methods for enzymatic nucleic acid amplification in vitrohave been developed and can be adapted to detect known sequencevariants. These include polymerase chain reaction (PCR) (Saiki et al.,1985; Saiki et al., 1988), ligase chain reaction (LCR) (Landegren etal., 1988; Barany, 1991) and rolling circle amplification (RCA) (Lizardiet al., 1998; Baner et al., 1998). PAP is different in many ways: i)pyrophosphorolysis and polymerization are serially coupled for eachamplification, ii) there is at least one dideoxyoligonucleotide for PAP.Other chemically modified nucleotides lacking the 3′-hydroxyl group atthe 3′ terminus, such as acyclonucleotides can serve the same function(see Example 12 below), iii) one format is for linear amplification andthe other is for exponential amplification, iv) PP_(i) is necessary forthe amplification, v) significant nonspecific amplification requiresboth mismatch pyrophosphorolysis and misincorporation, vi) PAP candetect known point mutations and greatly increase the specificity todetect an extremely rare mutant allele from the wild-type allele.

The mechanistic basis is that two or more reactions are serially coupledfor amplification with increased specificity. The key component of PAPis a pyrophosphorolysis activatable oligonucleotide. The blocked 3′terminus in these experiments is a dideoxy nucleotide, but anynon-extendible nucleotide susceptible to pyrophosphorolysis could inprinciple be substituted. Indeed, any enzyme that cleaves anoligonucleotide 5′ to a mismatch could serve the same function aspyrophosphorolysis activation. For example, a blocked oligonucleotideincluding the methylated recognition sequence (such as G^(m)ATC) isannealed to its target with the unmethylated recognition sequence, thenrestriction endonuclease (such as DpnI) can only cleave the methylatedsite and so activate the oligonucleotide for extension. If a mismatch islocated 5′ to the cleavage site, significant nonspecific amplificationrequires the serial coupling of mismatch cleavage and amisincorporation, which is a rare event. Activatable oligonucleotidesmay also be combined with “minisequencing” primer extension. This mayprovide a more specific assay for detection of single base changes thatmight be particularly amenable to chip technology in which specificitycan be a problem (Syvanen, 1999). Demonstration that PAP can occur inthe linear format (FIG. 10) supports the feasibility of this approach.

Nucleoside triphosphates and 2′-deoxynucleoside triphosphates or theirchemically modified versions may be used as substrates formultiple-nucleotide extension by PAP, i.e., when one nucleotide isincorporated the extending strand can be further extended.2′,3′-dideoxynucleoside triphosphates or their chemically modifiedversions that are terminators for further extension may be used forsingle-nucleotide extension. 2′,3′-dideoxynucleoside triphosphates maybe labeled with radioactivity or fluorescence dye for differentiationfrom the 3′ terminal dideoxynucleotide of oligonucleotide P*. Mixturesof nucleoside triphosphates or 2′-deoxynucleotide triphosphates and2′,3′-dideoxynucleoside triphosphates may also be used.

In PAP, specific nucleic acid sequence is produced by using the nucleicacid containing that sequence as a template. If the nucleic acidcontains two strands, it is necessary to separate the strands of thenucleic acid before it can be used as the template, either as a separatestep or simultaneously. The strand separation can also be accomplishedby any other suitable method including physical, chemical or enzymaticmeans.

When it is desired to produce more than one specific product from theoriginal nucleic acid or mixture of nucleic acids, the appropriatenumber of different oligonucleotides are utilized. For example, if twodifferent specific products are to be produced exponentially, fouroligonucleotides are utilized. Two of the oligonucleotides (P*≧1) arespecific for one of the specific nucleic acid sequences and the othertwo oligonucleotides (P*≧1) are specific for the second specific nucleicacid sequence. In this manner, each of the two different specificsequences can be produced exponentially by the present process.

The DNA or RNA may be single- or double-stranded, may be a relativelypure species or a component of a mixture of nucleic acids, and may belinear or circular. The nucleic acid or acids may be obtained from anysource, for example, from plasmid, from cloned DNA or RNA, or fromnatural DNA or RNA from any source, including bacteria, yeast, viruses,and higher organisms such as plants or animals. DNA or RNA may beextracted from blood, tissue material such as chorionic villi oramniotic cells by a variety of techniques such as that described byManiatis et al. (1982).

The P* oligonucleotides are selected to be “substantially complementary”to the different strands of each specific sequence to be amplified.Therefore, the P* oligonucleotide sequence need not reflect the exactsequence of the template. For example, a non-complementary nucleotidesegment may be attached to the 5′-end of the P* oligonucleotide, withthe remainder of the P* oligonucleotide sequence being complementary tothe strand. Alternatively, non-complementary bases or longer sequencescan be interspersed into the P* oligonucleotide, provided that the P*oligonucleotide sequence has sufficient complementarity with thesequence of the strand to be amplified to hybridize therewith and form atemplate for synthesis of the extension product of the other P*oligonucleotide. As used in the claims, the term “complementary” shouldbe understood to mean “substantially complementary,” as discussedherein.

Any specific nucleic acid sequence can be produced by the presentprocess. It is only necessary that a sufficient number of bases at bothends of the sequence be known in sufficient detail so that twooligonucleotides can hybridize to different strands of the desiredsequence at relative positions along the sequence. The greater theknowledge about the bases at both ends of the sequence, the greater canbe the specificity of the oligonucleotides for the target nucleic acidsequence, and thus the greater the efficiency of the process. It will beunderstood that the word oligonucleotide as used hereinafter may referto more than one oligonucleotide, particularly in the case where thereis some ambiguity in the information regarding the terminal sequence(s)of the segment to be amplified.

The present invention can be performed in a step-wise fashion whereafter each step new reagents are added, or simultaneously, where allreagents are added at the initial step, or partially step-wise andpartially simultaneous, where fresh reagent is added after a givennumber of steps. The simultaneous method may be utilized when anenzymatic means is used for the strand separation step. In thesimultaneous procedure, the reaction mixture may contain thestrand-separating enzyme (e.g., helicase), an appropriate energy sourcefor the strand-separating enzyme, such as ATP. Additional materials maybe added as necessary.

The nucleic acid polymerase may be any compound or system that willfunction to accomplish the amplification. Suitable enzymes for thispurpose include, for example, Tfl DNA polymerase, Taq DNA polymerase, E.coli DNA polymerase I, Klenow fragment of E. coli DNA polymerase I, T4DNA polymerase, T7 DNA polymerase, other available DNA polymerases, RNApolymerases or their variants, reverse transcriptase or its variants,and other genetic engineered versions. It is predicted on the basis ofthe relationship between reverse and forward reactions that a DNApolymerase will have high and even pyrophosphorolysis activity for theP* activatable oligonucleotide, if it incorporates ddNTPs efficiently(compared with dNTPs) and evenly (compared among the four ddNTPs). Ofall the DNA polymerases, the genetic engineered version may be the bestin the future, such as ThermoSequenase (Vander Horn et al., 1997).Generally, the synthesis will be initiated at the 3′ end of eacholigonucleotide and proceed in the 5′ direction on the template strand.However, inducing agents which initiate synthesis at the 5′ end andproceed in the other direction can also be used in the PAP method asdescribed above.

Example 2 Preparation of Template by PCR

A 640-bp region of the human D₁ dopamine receptor gene was amplified byPCR with two primers (T=5′ GAC CTG CAG CAA GGG AGT CAG AAG 3′ (SEQ IDNO:1) and U=5′ TCA TAC CGG AAA GGG CTG GAG ATA 3′ (SEQ ID NO:2)). TheTU:UT duplexed product spans nucleotides 33 to 672 in GenBank X55760 andthe G+C content of the product is 55%. A common A to G polymorphism islocated at nucleotide 229, resulting in three genotypes of G/G, A/A andG/A. The PCR volume is 50 μl: 50 mM KCl, 10 mM Tris/HCl, pH 8.3, 1.5 mMMgCl₂, 200 μM each of the four dNTPs, 0.1 μM of each primer, 2% DMSO, 1U of Taq DNA polymerase (Boehringer Mannheim) and 250 ng of genomic DNAfrom G/G homozygote, A/A homozygote or G/A heterozygotes. Cyclingconditions included: denaturation at 94° C. for 15 sec., annealing at55° C. for 30 sec., and elongation at 72° C. for one min., for a totalof 35 cycles with a GeneAmp PCR System 9600 (Perkin-Elmer AppliedBiosystems). The PCR product was purified from primers and other smallmolecules by approximately 10,000-fold by three times of retention on aCentricons 100 microconcentrator (Amicon). The amount of recovered PCRproduct was determined by UV absorbance at 260 nm.

Synthesis of P* by Adding a 3′ Dideoxynucleotide

The deoxynucleotide oligonucleotide was synthesized by PerseptiveBiosystems 8909 Synthesizer (Framinsham) and purified by oligopurecartridges (Hamilton) in the City of Hope DNA/RNA Chemistry Laboratory.The 3′ terminal dideoxynucleotide was added by terminal transferase. Themixture contained a total volume of 30 μl: 100 mM potassium cacodylate(pH 7.2), 2.0 mM CoCl₂, 0.2 mM DTT, 2500 μM of the oligonucleotide, 2 mM2′,3′-ddNTP (the molar ratio of the 3′-OH terminus to ddNTP was 1:24)(Boehringer Mannheim), 100 U of terminal transferase (GIBCO BRL). Thereaction was incubated at 37° C. for 4 hr and then stopped by addingEDTA at 5 mM final concentration. After desalting using a Centri-Spin™column (Princeton Separations), P* was purified by preparative 7 Murea/20% polyacrylamide gel electrophoresis in TBE buffer (90 mMTris/borate, 1 mM EDTA, pH 8.3) (Maniatis et al., 1982). The amount ofthe recovered P* was determined by UV absorbance at 260 nm.

Since small amounts of unterminated oligonucleotide would result innonspecificity of pyrophosphorolysis, each P* was ³²P-labeled at the 5′terminus by T4 polynucleotide kinase and then was electrophoresedthrough a 7 M urea/20% polyacrylamide gel. Only P* products were visibleeven when the gel was overexposed. It is estimated that more than 99.99%of P* contained a dideoxynucleotide at the 3′ terminus. The purity of P*was supported by the absence of PCR product or PAP product at pH 8.3.

Pyrophosphorolysis Activated Polymerization

Regions from 445 to 469 bp within the TU:UT duplexed template wereamplified by PAP with oligonucleotides P* and U, or with only P*. ThePU:UP duplexed product corresponds to nucleotides 204-228 to 672 inGenBank X55760 and its G+C content is 56%. The PAP reaction mixturecontained a total volume of 25 μl: 50 mM KCl, 10 mM Tris/HCl (pH 7.6),1.5 mM MgCl₂, 100 μM each of the four dNTPs (dATP, dTTP, dGTP and dCTP),0.1 μM P*, 0.1 μM U oligonucleotide (TCATACCGGAAAGGGCTGGAGATA (SEQ IDNO:2)), 300 μM Na₄PP_(i), 2% DMSO, 1 μCi of [α-³²P] dCTP (3000 Ci/mmole,Amersham), 1 U of AmpliTaqFS DNA polymerase (PE Applied Biosystems) or0.5 U of each of AmpliTaqFS and Taq DNA polymerases, and 10 ng of TU:UT.ThermoSequenase (Amersham Pharmacia) was also tested under the sameconditions except for 8 U ThermoSequenase or 4 U ThermoSequenase plus0.5 U Taq and 2.5 mM MgCl₂. The cycling conditions included:denaturation at 94° C. for 10 sec., annealing at 60° C. for 1 min. (at55° C. for ThermoSequenase), and elongation at 72° C. for 2 min., for atotal of 15 cycles.

The product was electrophoresed through a standard 2% agarose gel. Thegel was stained with ethidium bromide for UV photography by a CCD camera(Bio-Rad Gel Doc 1000) and Multi-Analyst® software, dried and subjectedto Kodak X-OMAT™ AR film for autoradiography. The PAP yield wasquantitated with a PhosphorImager with ImageQuant software (MolecularDynamics) as the total number of pixels in the PCR band minus thebackground, indicated as a random unit.

Enhanced PAP Efficiency

In Example 1, only the P* with ddG at the 3′ terminus was amplifiedusing native Tfl or Taq DNA polymerase. AmpliTaqFS and ThermoSequenaseDNA polymerases were found to achieve much higher PAP efficiency withmuch less discrimination against any kind of dideoxynucleotide (ddAMP,ddTMP, ddGMP or ddCMP) at the 3′ terminus of P*. For example,P*(212)18G⁰ and P*(212)18A⁰, which are 18-mers of the dopamine D₁receptor gene but have ddGMP and ddAMP at the 3′ termini (Table 3),specifically amplified the G and A alleles, respectively. Their yieldratio was 1.4 (compare lanes 9 with 11 in FIG. 11B), and so P*(212)18G⁰is estimated to be 4% more efficient per cycle than P*(212)18A⁰. AnotherP*(228)26A⁻²⁴=5′ TAGGAACTTGGGGGGTGTCAGAGCCC* 3′ (SEQ ID NO:12), which isa 26-mer with ddCMP at the 3′ terminus, was amplified as efficiently asa primer without ddCMP at the 3′ terminus, and the yield was estimatedto be increased 1,000 fold compared with that by using Tfl or Taq.Moreover, PAP amplified segments directly from human genomic DNA.

TABLE 3 PAP specificity affected by P* length and mismatch MismatchNoise base T_(m) ratio Name Sequence (SEQ ID NO:) Type Distance^(c) (°C.)^(d) (%)^(e)                                     G Template Strand 5′. . . AATCTGACTGACCCCTATTCCCTGCTT GGAAC . . . 3′ (3)                                    A P*(204)26G^(0a)         5′tctgactgACCCCTATTCCCTGCTTG*^(b )(13) G 0 80 0.0 P*(208)22G⁰             5′actgACCCCTATTCCCTGCTTG* (14) G 0 68 0.5 P*(210)20G⁰               5′tgACCCCTATTCCCTGCTTG* (15) G 0 62 0.1 P*(212)18G⁰                 5′ACCCCTATTCCCTGCTTG* (16) G 0 56 0.3 P*(216)26G⁻¹²         5′ctattcccTGCTT G GGAACTTGAGGG* (17) G −12 80 107.1P*(220)22G⁻¹²              5′tcccTGCTT G GGAACTTGAGGG* (18) G −12 7095.5 P*(222)20G⁻¹²                5′ccTGCTT G GGAACTTGAGGG* (19) G −1264 75.8 P*(224)18G⁻¹²                  5′TGCTT G GGAACTTGAGGG* (20) G−12 56 7.0 P*(206)26A⁻²          5′tgactgacCCCTATTCCCTGCTTAGG* (21) A −280 30.4 P*(210)22A⁻²              5′tgacCCCTATTCCCTGCTTAGG* (22) A −2 683.3 P*(212)20A⁻²                5′acCCCTATTCCCTGCTTAGG* (23) A −2 62 2.0P*(214)18A⁻²                  5′CCCTATTCCCTGCTTAGG* (24) A −2 56 0.0P*(206)26G⁻⁹          5′tgactgacCCCTATTC G CTGCTTAGG* (25) C→G −9 8095.0 P*(210)22G⁻⁹              5′tgacCCCTATTC G CTGCTTAGG* (26) C→G −968 88.1 P*(212)20G⁻⁹                5′acCCCTATTC G CTGCTTAGG* (27) C→G−9 62 49.5 P*(214)18G⁻⁹                  5′CCCTATTC G CTGCTTAGG* (28)C→G −9 56 4.7 P*(206)26T⁻¹⁵          5′tgactgacCC TTATTCCCTGCTTAGG* (29) C→T −15 78 89.0 P*(210)22T⁻¹⁵             5′tgacCC T TATTCCCTGCTTAGG* (30) C→T −15 66 47.8P*(212)20T⁻¹⁵                5′acCC T TATTCCCTGCTTAGG* (31) C→T −15 603.4 P*(214)18T⁻¹⁵                  5′CC T TATTCCCTGCTTAGG* (32) C→T −1554 0.0 ^(a)P*(204)26G⁰ is a P* with a G dideoxynucleotide at the 3′terminus. “0” means the allele-specific base is at the 3′ terminus. Thefirst base at 5′ terminus corresponds to nucleotide 204 in GenBankX55760. Its length is 26 bases. ^(b)The bold G or A are the G or Aallele specific base and the underlined base is designed mismatch.^(c)The distance from the 3′ terminus to the allele-specific base: “0” =at the 3′ terminus, −3 = three bases from the 3′ terminus. ^(d)The Tmfor oligonucleotide was estimated to be 4° C. X (G + C) + 2° C. X (T +A) under condition of 1M NaCl. The length of each P* is 18 bases.^(e)The noise rate of PAP (%) is defined as the relative yield ofnon-specific allele product to specific allele product by the same P*,or as the relative yield of the designated mutated P* to its native formby using the same template. A specific signal is denoted as <10% noiserate.

AmpliTaqFS has two mutations compared with native Taq. One mutation inthe 5′ nuclease domain eliminates 5′-3′ exonuclease activity and thesecond mutation F667Y in the active site (Innis and Gelfand, 1999).ThermoSequenase has the same mutation F667Y in the active site but adeletion of the 5′-3′ exonuclease domain (Tabor and Richardson, 1995;Van der Horn et al., 1997). They do not distinguish between dNTP andddNTP for incorporation. The pyrophosphorolysis of ddNMPs, which is thereverse reaction, is supposed to be much higher and less discriminatedby these enzymes. Although either AmpliTaqFS or ThermoSequenase DNApolymerases used was formulated to contain a thermostablepyrophosphatase (manufacturers' instructions) that can hydrolyze PP_(i)in the reaction so as to decrease PAP efficiency, PAP was stillamplified under our conditions. AmpliTaqFS and ThermoSequenase DNApolymerases will work better in their pure form without the contaminatedpyrophosphatase.

The 3′ Specific Subsequence of P*

Various P*s were examined with different lengths and mismatches usingAmpliTaqFS (Table 3). The effect of length and mismatch on PAPefficiency is expressed as the relative yield (%) between two P*s ofdifferent lengths from the same template (FIG. 12), which varied from0.0% to 201.5% with each two to four less bases in length. Thespecificity of PAP is also affected by P* length and mismatch (Table 3).The noise rate (%) is defined as the relative yield of the mismatchproduct to the match product, and a specific signal is scored with <10%noise rate. If the allele-specific base of P* was at the 3′ terminus,only the specific allele was amplified and the specificity was notassociated with P* length (FIG. 12A). If the allele-specific base wasnot at the 3′ terminus of P*, the specificity was associated with P*length. Any non-3′-terminal mismatch in the 18-mer P*, which was up to15 bases from the 3′ terminus, caused no amplification (FIGS. 12B-12E),but even two such mismatches in the 26-mer P* caused non-specificamplification.

The 18-mers were further examined using “stacked” P*s, which span theallele-specific base at different positions (FIG. 13 and Table 4). Thenoise rate (%) varied from 0.0% to 7.1%. The length of the 3′ specificsubsequence was ≧13 bases.

TABLE 4 PAP specificity with differently positioned P*s NameSequence (SEQ ID NO:)                         G Template5′GACTGACCCCTATTCCCTGCTT-GGAACTTGAGGGGTGTC . . . 3′ (33)                        A P*(212)18G⁰      5′ACCCCTATTCCCTGCTTG* (16)P*(212)18A⁰      5′ACCCCTATTCCCTGCTTA* (34) P*(214)18A⁻²       5′CCCTATTCCCTGCTTAGG* (24) P*(218)18G⁻⁶            5′TTCCCTGCTTGGGAACT* (35) P*(221)18G⁻⁹              5′CCCTGCTTGGGAACTTGA* (36) P*(224)18G⁻¹²                 5′TGCTTGGGAACTTGAGGG* (37) Allele-specificNoise rate (%)^(a) 3′ terminal base Exponential Linear PAP Name dideoxyType Distance Tm (° C.) PAP template P*(212)18G⁰ ddG G 0 56 2.7 0.0P*(212)18A⁰ ddA A 0 54 3.8 1.1 P*(214)18A⁻² ddG A −2 56 4.7 0.0P*(218)18G⁻⁶ ddT G −6 54 0.0 0.0 P*(221)18G⁻⁹ ddA G −9 56 1.7 1.7P*(224)18G⁻¹² ddG G −12 56 7.1 0.6 ^(a)The amplification from the G andA templates by PAP with two oligonucleotides or linear PAP with one P*.The noise rate of PAP (%) is the relative yield of the non-specificallele product to the specific allele product.

Similar results were obtained by using P*s which match and mismatch theG allele at different positions (Table 5). The noise rate with onemismatch was various from 0.8% to 5.6%. The length of the 3′ specificsubsequence was ≧16 bases. The noise rate with two mismatches was 0%(compare lane 2 with lanes 10-15 in FIG. 14).

TABLE 5 PAP specificity with differently mismatched P*sNoise rate (%)^(b) The 3′ terminal Mismatch^(a) Exponential Linear NameSequence (SEQ ID NO:) dideoxy Type Distance T_(m )(° C.) PAP PAPP*(212)18G⁰ 5′ACCCCTATTCCCTGCTTG* (16) DdG 56 1.0 0.0 P*(212)18A⁻³5′ACCCCTATTCCCTG A TTG* (38) DdG C→A −3 54 1.3 0.0 P*(212)18G⁻⁶5′ACCCCTATTCC G TGCTTG* (39) DdG C→G −6 56 0.8 0.6 P*(212)18C⁻⁹5′ACCCCTAT C CCCTGCTTG* (40) DdG T→C −9 58 1.8 0.4 P*(212)18G⁻¹² 5′ACCCCG ATTCCCTGCTTG* (41) DdG T→G −12 58 5.6 1.7 P*(212)18T⁻¹⁵ 5′AC TCCTATTCCCTGCTTG* (42) DdG C→T −15 54 3.3 1.2 ^(a)match or mismatch withthe G allele. ^(b)noise rate (%) is the relative yield between amismatched P* and P*(212)18G⁰ with the G allele-specific template.

Linear PAP was examined using only 18 mer P*s and higher specificity wasobserved with lower noise rate (Tables 4 and 5). Linear PAP takes adifferent mechanistic pathway in which every non-specific product isgenerated from the starting template which requires mismatchedpyrophosphorolysis with the 3′ terminal mismatched P*, or bothmismatched pyrophosphorolysis and mismatched extension with the non-3′terminal mismatched P*.

PASA was performed with 17-mer primers without adding a ddNMP at the 3′terminus (see Tables 4 and 5). A mismatched 17-mer primer stronglyamplified a nonspecific product with 30% noise rate when the mismatchwas as near as 6 bases to 3′ terminus, showing a much shorter 3′specific subsequence. Similar results were reported elsewhere previously(Sarkar et al., 1990).

In summary, P* (1-length) has two subsequences: a 3′ specificsubsequence (n=the number of bases of the 3′ specific subsequence ≦1)determines the specificity, i.e., within this region any mismatch to itscomplementary strand of the template results in no substantialamplification; and a 5′ enhancer subsequence (m=the number of bases of5′ enhancer subsequence ≧0) enhances the amplification efficiency. PAPspecificity is co-determined by the base pairing specificity of the 3′specific subsequence, the pyrophosphorolysis specificity and thepolymerization specificity. Thus, the base pairing specificity of the 3′specific subsequence is a minimum requirement of the PAP specificity.

The length of the 3′ specific subsequence of P* may be affected by thesequence context and size of the P*, the type of the 3′ terminaldideoxynucleotide, the template sequence, the DNA polymerase, othercomponents like ion, and cycling conditions. When the template containsrepeated sequences >1 or homogeneous polymer runs >1, P* losesspecificity for anchoring. The length of the 3′ specific subsequence ofP* may be affected by the sequence context and size of the P*, the typeof the 3′ terminal dideoxynucleotide, the template sequence, the DNApolymerase, other components like ion, and cycling conditions. When thetemplate contains repeated sequences >1 or homogeneous polymer runs >1,P* loses specificity for anchoring.

Scanning or Resequencing for Unknown Sequence Variants

The property of the 3′ specific subsequence of P* can be applied toscanning for unknown sequence variants or re-sequencing of predeterminedsequences in a parallel way. Each nucleotide on the complementary strandof the predetermined sequence is queried by four downstream P*s, such as18-mers (FIG. 11), which have identical sequence except that at the 3′terminus, either ddAMP, ddTMP, ddGMP or ddCMP corresponds to thewild-type sequence and the three possible single base substitutions. Thenumber of P*s scanning the complementary strand of X bases ismultiplication of 4 and X, which is suitable for either exponential orlinear PAP. The four downstream P*s can even be immobilized on a singledot when ddAMP, ddTMP, ddGMP and ddCMP at the 3′ termini are labeleddifferently for differentiation, such as by four fluorescence dyes. Theamplification signal can thus be represented by intensity decrease ofeach dye when ddNMP is removed from P* by pyrophosphorolysis. Oneadvantage of linear PAP is that the four ddNTPs can be used assubstrates for single base extensions, which are labeled with differentdyes for differentiation.

Briefly, if only all the P*s corresponding the wild-type sequence arespecifically amplified, the wild-type sequence can be arranged in orderby analyzing overlaps. A P* with a single base substitution at the 3′terminus is amplified at the position of hemi- or homo-point mutations.The mutation also creates a “gap” of no PAP signal, which spans a regionof several successive nucleotides. For single base substitution, the gapsize (bases)+1=the length of the 3′ specific subsequence.

Furthermore, we can also scan the sense strand by designing a second setof upstream P*s. An unknown single base substitution can be determinedby combination of the two sets of P*s, even in heterozygotes. An unknownsmall deletion and insertion can be detected and localized. In order toidentify a specific type of deletion or insertion, it is possible to addcorresponding P*s. For fingerprinting, which can provide information ofmutation position, there is a simple stacking way that the stackedregion of each two successive P*s<the 3′ specific subsequence on thearray to reduce the number of P*s by up to n fold.

Determination of De Novo DNA Sequence

The concept of de novo DNA sequencing by PAP makes use of all thepossible 3′ specific subsequences of P* to identify the presence of the3′ specific subsequence in de novo sequence. A complete set of the 3′specific subsequences of P* is 4^(n). Each of the 3′ specificsubsequence has a complete subset of the 5′ enhancer subsequence of4^(m). For example, a complete set of 16-mer as the 3′ specificsubsequence and 2-mer as the 5′ enhancer subsequence can be indicated as(A, T, G, C)(A, T, G, C) N₁₆=4¹⁸.

Briefly, the procedure first determines the list of all the specific PAPamplifications and then reconstructs the unknown DNA complementarysequence from this list by ordering the 3′ specific subsequences withthe given length by using the Watson-Crick pairing rules.

The assembly process is interrupted wherever a given 3′ specificsubsequence of P* is encountered two or more times. One of the factorsinfluencing the maximum sequencing length is the length of the 3′specific subsequence. The length of a random sequence that can bereconstructed unambiguously by a complete set of the 3′ specificsubsequence with the given length is approximately the square root ofthe number of the 3′ specific sequence in the complete set with ≧50%possibility that any given 3′ specific subsequence is not encounteredtwo or more times. Octamers of the 3′ specific subsequence, of whichthere are 65,536, may be useful in the range up to 200 bases.Decanucleotides, of which there are more than a million, may analyze upto a kilobase de novo sequence. 18 mer P*s containing 16 mer as the 3′specific subsequence, which complete set is 418 of P*s, may sequencemaximum 77,332 bases.

When there is neighbored known sequence to design an oppositeoligonucleotide for PAP with two oligonucleotides. The maximumsequencing length is mainly limited to the opposite oligonucleotide, butnot to the length of the 3′ specific subsequence of P*, termedConditional de novo DNA sequencing.

Other Applications for PAP

For fingerprinting which compares two DNA sequences to see if they arethe same or different, there is a simple way to reduce the number of P*sby using an incomplete set of the 3′ specific subsequences. By arrangingthem in a particular order, it is possible to identify the chromosomallocations as well as sequences. Considering the 3×10⁹ bp DNA in humangenome, PAP with two oligonucleotides is preferred over PAP with onlyone P* to increase the specificity.

To monitor gene expression profiling, where up to 6×10⁴ to 10⁵transcripts are expressed and details of the precise sequence areunnecessary, PAP with only one P* can be applied and a set of P* whichidentify unique motifs in genes can be designed with a total length ofup to 22-mer. Between each two P*s, there is at least a sequencedifference at the 3′ terminus or ≧2 sequence differences at the non-3′terminus.

Comparison with Sequence by Hybridization

In SBH by using oligonucleotide, the DNA sequence is determined by thehybridization and assembly of positively hybridizing probes throughoverlapping portions. It has been known for a long time that a singleoligonucleotide hybridization on a immobilized sample can be veryspecific in optimal hybridization and washing conditions (Wallace etal., 1979), thus it is possible to discriminate perfect hybrids fromones containing a single internal mismatch. The oligonucleotides inarray are 11-20 nucleotides in length and have 7-9 bases specific regionin the middle, the non-specific signal is generated by mismatchedhybridization. Under standard hybridization and washing conditions, theduplex stability between match and mismatch is also affected by theterminal mismatch and the flanking sequence (Drmanac et al., 1989;Khrapko et al., 1989; Ginot, 1997).

SHB can be modified with enzymes in several ways (Miyada and Wallace,1987; Southern, 1996). Primer extension by DNA polymerase incorporatesbases one at a time only if they match the complement strand. Ligase hassimilar requirements: two oligonucleotides can be joined enzymaticallyprovided they both are complementary to the template at the position ofjoining.

FIGS. 11A-11B show the enhancement of PAP efficiency. FIG. 11A. PAP isamplified with two oligonucleotides P* and U from duplex TU:UT template.Each of the four P*s has a ddA, ddT, ddG and ddC at the 3′ terminus. The3′ terminal base is either specific to the complementary strand of the Gor A alleles, or not matched. FIG. 11B. Autoradiogram of PAP from theG/G, A/A and G/A genotypes of the human dopamine receptor gene. Theradioactively labeled specific products of 461 bases (duplex PU:UP andexcess antisense strand UP) are produced. Other side products UT andUT:TU are indicated. Note that TU:UT derives from annealing of excessradioactively labeled UT with non-radioactively labeled TU originaltemplate.

FIGS. 12A-12E show the effect of P* length and mismatch on PAPefficiency. PAP was amplified with P* and U oligonucleotide (see Table3). In each of FIGS. 12A-12E, P*s have the sample 3′ termini but aredifferent in length. FIG. 12A. In lanes 1-4, the P*s matched andamplified the G allele. In lanes 5-8, the P*s mismatched at the 3′termini but amplified the A allele. FIG. 12B. In lanes 9-12, the P*smatched and amplified the G allele. In lanes 13-16, the P*s mismatchedat −12 bases to the 3′ termini but amplified the A allele. FIG. 12C. Inlanes 17-20, the P*s matched and amplified the A allele. In lanes 21-24,the P*s mismatched at −2 bases to the 3′ termini but amplified the Gallele. FIG. 12D. In lanes 25-28, the P*s mismatched at −9 bases to the3′ termini but amplified the A allele. FIG. 12E. In lanes 29-32, the P*smismatched at −15 bases to the 3′ termini but amplified the A allele.The length effect is indicated as the yield ratio in one lane (L_(n)) tothe previous lane (L_(n-1)). The length effect was not shown in lanes5-8 because the signals are at or close to the background.

FIG. 13 shows PAP specificity with differently positioned P*s. PAP wasamplified with a P* and U oligonucleotide (see Table 4). The P* matchedto and amplified the G allele in lanes 2-7, but mismatched to andamplified the A allele in lanes 9-15. Lanes 1 and 9 were PCR controlwith D₁(212)17 mer and U. Lanes 8 and 16 were extension control withonly U.

FIG. 14 shows PAP specificity with differently mismatched P*s. PAP wasamplified with a P* and U oligonucleotide (see Table 5). In lanes 2-7,the P* amplified the G allele with match or one mismatch. In lanes 9-15,the P* amplified the A with one or two mismatches. Lanes 1 and 9 werePCR control with D₁(212)17 mer and U. Lanes 8 and 16 were extensioncontrol with only U.

Example 3

PAP Amplification from Genomic DNA

This example illustrates PAP amplification directly from genomic DNA.The oligonucleotides used in this example are listed below. Lane numbersrefer to lanes in FIG. 15.

The downstream oligonucleotides in 0.1 μM concentration are:

Lane 1: D₁(204)25D (SEQ ID NO: 43) 5′ TCTGACTGACCCCTATTCCCTGCTT 3′Lane 2: P*(206)24A⁰ (A allele specific; SEQ ID NO: 44) 5′GACTGACCCCTATTCCCTGCTTA* 3′ Lane 3: P*(204)26G⁰(G allele specific; SEQ ID NO: 45) 5′ TCTGACTGACCCCTATTCCCTGCTTG* 3′Lane 4: P*(206)24G⁻² (G allele specific; SEQ ID NO: 46) 5′ACTGACCCCTATTCCCTGCTTGGG* 3′ Lane 5: P*(228)26A⁻²⁴(A allele specific; SEQ ID NO: 47) 5′ TAGGAACTTGGGGGGTGTCAGAGCCC* 3′

The opposite upstream oligonucleotide in 0.1 μM concentration is:D₁(420)24 U 5′ ACGGCAGCACAGACCAGCGTGTTC 3′ (SEQ ID NO:48), which waspaired with each downstream oligonucleotide. See Footnotes of Table 3for details.

The other components were the same as in Example 2, except for thefollowing: 0.5 U of each of AmpliTaqFS and Taq DNA polymerases, and 100ng of heterozygous G/A allelic genomic DNA were used per 25 μl reactionby using 30 cycles.

The PAP product size range from 193 bp to 218 bp. One double strandedand one single stranded product was observed on the gel, indicating theexhaust of PP_(i) hydrolyzed by the contaminated thermostablepyrophosphatase.

Example 4 Comparison of Specificity of LM-PCR and LM-PAP

The LM-PCR protocol includes primer extension, linker ligation, PCRamplification, and directed labeling in the human dopamine D₁ receptorgene model system (FIG. 16). LM-PCR was performed with the addition byterminal deoxynucleotidyl transferase (TdT) (this protocol is known asTD-PCR) on UV-treated genomic DNA samples essentially as described(Pfeifer et al., 1999), except that Vent_(R) (exo-) DNA polymerase wasused in the first 10 cycles of primer extension (P1 primer=5′TTGCCACTCAAGCGGTCCTCTCAT 3′ (SEQ ID NO:49)). Temperature cycles were 1min at 95° C., 3 min. at 63° C., and 3 min at 72° C. To enhance thesignal, terminal transferase was added to the protocol, and thisvariation of LM-PCR is called TD-PCR. Dynabeads were used to enrichtarget DNA molecules before terminal deoxynucleotidyl transferase (TdT)tailing. PCR was performed using Expand Long Template PCR System 3 (BMB)as described by the manufacturer (P2 primer=5′ GAAGCAATCTGGCT GTGCAAAGTC3′ (SEQ ID NO:50)). The PCR products were purified using QIAquick PCRPurification Kit (QIAGEN) before performing the direct labeling. Aportion of the cleaned PCR product was used for direct labeling withAmpliTaq DNA Polymerase (Perkin-Elmer) with ³²P labeled primers:

P3A: (5′ TCTGACTGACCCCTATTCCCTGCTTA 3′ (SEQ ID NO: 51; the 3′terminal deoxynucleotide is A allele specific) and P3G: (5′TCTGACTGACCCCTATTCCCTGCTTG 3′. (SEQ ID NO: 52; the 3′terminal deoxynucleotide is G allele specific)

LM-PAP was performed as allele-specific PCR except for the directlabeling step by PAP (FIG. 16A). The purified PCR product was used fordirect labeling with ³²P labeled primers:

P3A: 5′ TCTGACTGACCCCTATTCCCTGCTTA* 3′ (SEQ ID NO: 53; the 3′ terminaldeoxynucleotide is A allele specific) and P3G: 5′TCTGACTGACCCCTATTCCCTGCTTG* 3′ (SEQ ID NO: 54; the 3′ terminaldeoxynucleotide is G allele specific)using PAP reaction conditions in a 10 μl volume (50 mM KCl, 10 mMTris/HCl (pH 7.6), 1.5 mM MgCl₂, 100 μM of each dNTP, 0.1 μM P*, 300 μMNa₄PP_(i), 2% DMSO, 0.25 U each of AmpliTaqFS and AmpliTaq DNAPolymerases (Perkin-Elmer). The cycling conditions were 94° C., 10 sec.;60° C., 1 min. and 72° C., 2 min. for a total of 8 or 16 cycles. LM-PAPwas dramatically more specific than LM-PCR. The initial data with thedopamine D1 gene shows a lower background with LM-PAP than with theidentical unblocked oligonucleotide with LM-PCR. Also, LM-PAP can beperformed with the PGK gene, a gene with a very high GC rich region(70%) (FIG. 16B).

FIG. 16A shows a UV footprinting of the dopamine D1 receptor gene with acomparison of allele-specific LM-PAP and allele-specific LM-PCR. Adirect comparison of LM-PAP with a P* and LM-PCR with an unblockedprimer of identical sequence shows that two alleles can be distinguishedwith LM-PAP, but not with LM-PCR. Both methods were performed on HF-16DNA that was untreated (C), in vitro treated (T) or in vivo treated (V)with UV. The direct labeling reaction using PAP conditions (lanes 7-18)with ³²P labeled primers P3A* (lanes 7-9 and 13-15) and P3G* (lanes10-12 and 16-18) was done with AmpliTaqFS and AmpliTaq for 8 and 16cycles. For LM-PCR the direct labeling reaction was done with AmpliTaq(lanes 1-6) and ³²P-labeled primers P3A (lanes 1-3) and P3G (lanes 4-6)for 8 cycles. Allelic primers P*s, P3A* and P3G* for LM-PAP clearlydistinguish the two alleles, while unblocked allelic primers ofidentical sequence, P3A and P3G, were unable to distinguish the allelesby LM-PCR.

FIG. 16B shows a UV footprinting of the pgK gene. The LM-PAP procedurefor PGK was essentially the same as for the dopamine D1 receptor exceptthat Pfu Turbo DNA polymerase was used in the primer extension, as wellas 7-deaza-dGTP/dGTP in a 3:1 ratio. Temperature cycles were 95° 1 min.,60° 2 min., and 76° 3 min. The PCR step was performed using Vent (exo-)DNA Polymerase at 97° 1 min., 60° 2 min., 76° 3 min. also with deazadGTP. The purified PCR products were used for direct labeling with the³²P P3G* and P3C* primers using PAP reaction conditions in a 25 μlvolume (50 mM KCL, 20 mM Hepes, pH 6.95, 10 mM (NH₄)₂SO₄, 1.5 mM MgCl₂,40 μM dNTP, 150 μM Na₄PPi, 4% DMSO, and 1 unit of AmpliTaq FS DNAPolymerase. The conditions for cycling were 94° 15 sec., 60° 30 sec.,and 72° 1 min. for 10 cycles.

Example 5 Optimization of PAP-A to Detect a Mutation in 1 of 10⁴-10⁵Templates

One μg of lambda phage DNA contains 2×10¹⁰ copies of template. Thespecificity of PAP is determined by mixing one part mutant lacItemplates with 10⁴ to 10⁵ parts control DNA templates, e.g., wild-typelacI. The specificity of PAP-A is a function of the error rate of thepolymerase, the purity of P* (<2×10⁻⁴ by current purification protocol)and the potential for damage of the DNA template in the extractionprocess. The yield and specificity of PAP is optimized by testing enzymetype and concentration and the concentrations of other components, suchas dNTP, PP_(i), Mg⁺⁺ or Mn⁺⁺. Hotstart PAP using antibody-activatedenzyme, such as DNA polymerase, at room temperature can be used toeliminate spurious amplifications.

Wild-type and mutant lambda phage DNA, which are used in the laboratoryas a model system to study spontaneous mutation in mammals, are preparedfrom infected E. coli SCS-8 cells (Nishino et al., 1996). The lambdaphage is grown under high fidelity conditions and DNA is isolated withcare under conditions with low rates of DNA damage (Stratagene manual)(Nishino et al., 1996; Hill et al., 1999).

The mutants include one example of each of the two types of transitions,the four types of transversions and a one-base nucleotide deletion. P*sspecific for each of the mutations is synthesized. These DNA templatesare used for reconstruction experiments in which mutated DNA is seriallydiluted into wild-type DNA. The spiked samples are used to optimizePAP-A. The most robust polymerases are chosen based on yield andspecificity using TaqFS, ThermoSequenase, and SequiTherm Excel II(Epicentre). Other components of the reaction are optimizedsystematically, including thermocycling parameters, oligonucleotidelength, and reagent concentrations of PP_(i), dNTP and Mg⁺⁺ or Mn⁺⁺.Quantitative detection of the yield of PAP product is achieved withautoradiography or fluorescence on a SSCP gel. These data aids in theoptimization of PAP-R and LM-PAP (below). The optimization of thesevarious parameters result in a specificity of 1 part in 10⁴-10⁵.

The optimized conditions are also tested for detecting mutations in thehuman factor IX gene by mixing human mutant genomic DNA templates withup to 10⁴ wild-type templates. As with the lambda experiment,exponential PAP is performed with appropriately designedoligonucleotides (using Oligo5 software) for 40 cycles and strong signalis achieved by autoradiography or by fluorescence detection.

Example 6 Optimization of PAP-R

In a model system, mismatches along the length of P* inhibitedactivation, even when the mismatch is two nucleotides from the 5′ end(FIG. 14). An additional set of 18 mers of P*s, whose 5′ termini weredisplaced 2, 6, 9, and 12 nucleotides downstream, also showed inhibitionof activation (FIG. 13). In addition, 20 and 22 mers also showinhibition with single nucleotide mismatches (FIG. 12). To extend thesefindings and to lay the foundation for a robust method of resequencing,the relationship between the location of single base mismatches andactivation of P*s is analyzed further.

The factor IX gene is used as a model system because more than 1,000 DNAsamples from hemophilia patients and family members have beenascertained from previous work on the molecular epidemiology of germlinemutations in humans (Sommer, 1995; Ketterling et al., 1999). Two20-nucleotide regions of exon B and exon H in the human factor IX geneare used as model systems. The region of exon B is designed fromnucleotides 6460 to 6479 (5′ CGAGAAGTTTTTGAAAACAC 3′ (SEQ ID NO:55;Yoshitake et al., 1985), within which eight different single basemutations are available. The region of exon H is from nucleotides 30845to 30864 (5′ GAACATACAGAGCAAAAGCG 3′ (SEQ ID NO:56), within which sevenmutations at different positions are available. P*s identical towild-type regions B and H will be synthesized. Identical P*s aresynthesized, with the exception of a single nucleotide mismatch.

The wild-type factor IX sequence is used in the initial studies. A fewP*s that match the wild-type sequence or that mismatch at selected siteswithin the 5′ third of the oligonucleotide sequence are helpful inperforming pilot experiments to assess the optimal length of theoligonucleotide. The effects of polymerases and reaction conditions canbe assessed.

From preliminary data, it appears that 18 mers or larger may be anoptimal size. It is also possible that 25 mers or even 30 mers may beoptimal. For the present example, it is assumed that 20 mers are anoptimal size. Wild type P* and twenty P*s with one of the possiblesingle base mismatches at each nucleotide of the position region of exonB are synthesized. Eight of these P* are a perfect match to a mutationin a patient with hemophilia B. As positive controls, it is shown thatthese P*s activate efficiently when the appropriate mutated DNA sampleis used. Exponential PAP and linear PAP are performed and the noise rateis determined. The noise rate for linear PAP is generally lower and isused.

To confirm preliminary data in another sequence context, a similarexperiment is performed in exon H. The seven mutations in that region ofexon H are analyzed in a blinded manner to determine if the precisematch is detected. The effects of the position of the mismatch or thetype of mismatch on P* activation is determined. The effects ofdifferent polymerases, reaction temperature, and other reactionconditions can also be determined. Another set of 20 P*s providesadditional data from mismatches 12-20 nucleotides from the 3′ terminus.

Example 7 Optimization of LM-PAP

The human dopamine D₁ receptor gene and the mouse Pgkl gene are used asmodel systems to compare the analysis of chromatin structure when LM-PAPor LM-PCR is utilized. The dopamine D₁ receptor gene has been describedabove. X chromosome inactivation occurs at an early embryonic stage.Since the two alleles in female cells maintain a different expressionstatus, this is an advantageous system for studies of gene regulation.Pgkl is an X-linked housekeeping gene encoding phosphoglycerate kinase(PGK). PGK is an important enzyme in glycolysis and the gene is expectedto be active all the time except in the inactive X chromosome (Xi) offemale somatic cells and in male germ cells.

The preliminary data shows a dramatic enhancement of specificity withLM-PAP relative to LM-PCR in the dopamine D₁ receptor gene, a gene notpreviously analyzed for chromatin structure (FIG. 16A). In this example,LM-PAP and LM-PCR are performed. Three sets of oligonucleotides thatgenerated LM-PCR profiles and seven sets of primers that generatedLM-PCR profiles with unacceptable background in the Pgkl (and otherX-chromosomal genes) are used to compare LM-PAP with LM-PCR.Deoxy-terminating and dideoxy-terminating oligonucleotides of identicalsequence are utilized to perform LM-PAP and LM-PCR, respectively. Thelevel of signal relative to background is also quantitated by aPhosphoImager. The average signal-to-noise ratio is determined.Optimization data derived from analyses with PAP-A and PAP-R are alsouseful in the LM-PAP protocol. LM-PAP is optimized for the two regionsto determine if the signal-to-noise ratio can be reduced further.

Example 8 Optimization of Allele-Specific LM-PAP

Polymorphic sites of pgkla and 1b gene in both coding and non-codingregions have been reported (Boer et al., 1990). These are used to designthe allele-specific P*. One allele-specific oligonucleotide is chosenprospectively from the Pgkl gene and one is chosen prospectively fromthe dopamine D₁ receptor gene. Blocked and unblocked oligonucleotides ofidentical sequence are synthesized and allele-specific LM-PAP and LM-PCRare performed, respectively. The signal to noise ratio is quantitatedand compared.

Example 9 PAP-R on a Microarray

The initial experiment will focus on the two 20 nucleotide regions ofexons B and H as described above. The experimental design of PAP-R issimilar to the experiments described above, except for digitallight-direct synthesis of P* oligonucleotides on a microarray, e.g.,with the Geniom® instrument. A total of 160 oligonucleotides aresynthesized complementary to wild-type and to all the single basemismatches for 20 bp regions of exons B and H of the factor IX gene. Asa positive control, 160 oligonucleotides, each out of registered by onenucleotide, are synthesized to match exactly an adjacent 160 bp regionof the factor IX gene. Genomic DNA from wild-type and mutant samples isamplified, annealed to the oligonucleotides and primer extension will beperformed with a fluorescent dideoxy terminator. The protocol isoptimized for the solid support. Adjustment of primer length, enzymeutilized and reaction conditions is performed such that most, if notall, of the oligonucleotides that mismatch the two 20 bp nucleotideregions of factor IX generate little if any signal, while most of the160 control oligonucleotides generate a strong signal.

One strategy for resequencing is shown in FIGS. 3 and 4. Each nucleotidein the complementary strand of the predetermined sequence is queried byfour downstream P*s, such as 20 mers, which have identical sequenceexcept for the 3′ terminus, which is either ddA, ddT, ddG or ddC. For a1 kb segment, 4,000 P*s are needed in the downstream direction. In thesecond set of experiments, exons B and H of the factor IX gene areresequenced. Samples from more than 200 patients with differentmutations in these regions are available for analysis. False positivesand false negatives are assessed by blinded analysis. Heterozygousfemale samples are available for many of the mutations. For theremaining male patient samples one to one mixing experiments withwild-type or a second mutated sample generates the equivalent ofheterozygotes or compound heterozygotes, respectively. Subsequently, allthe regions of likely functional significance (the putative promoterregion, the coding regions, and the splice junctions) are resequenced(2.2 kb). Since more than 600 independent mutations are available, it ispossible to determine whether more than 99% of all sequence changes areidentified (the sequence changes in these samples have been determinedby direct sequencing over the course of a decade).

A P* with a single base substitution at the 3′ terminus generates asignal at the position of hemizygous or homozygous point mutations. Themutation also creates a “gap” of no PAP signal, which spans a region ofseveral successive nucleotides. When a single base substitution occurs,the gap size (nucleotides)+1=the length of the 3′ specific subsequence(FIGS. 3 and 4).

To analyze samples with higher G+C content (55%), mutations in the lacIgene are utilized. These mutations from the Big Blue® Transgenic MouseMutation Detection System, have the potential to facilitate thedefinition of a strategy that detects more than 99.9% of mutations,since more than 6,000 mutations are available in this system. Therelevant regions are analyzed with the help of robotic devices. Inaddition, hundreds of mutations or polymorphisms are available foranalysis in other genes with G+C contents of 30-75%. The dystrophin geneis particularly amenable to testing performance under conditions inwhich megabases of sequence require scanning. In this gene in which 90segments are amplified by a robotic device, virtually all sequencevariants have been defined by DOVAM-S followed by DNA sequencing. Thisis advantageous because many molecular epidemiological and moleculardiagnostic applications benefit from resequencing that detects virtually100% of the mutations.

Example 10 PAP Amplification Directly from Human and Mouse Genomic DNAs

PAP was performed with each of two P*s, P1* (SEQ ID NO:45, G allelespecific) or P2* (SEQ ID NO:47, A allele specific) and an upstreamunblocked primer (U; (SEQ ID NO:48)) to amplify 180-bp segments of theD₁ dopamine gene. The P* are 26-mers with ddC and ddG at the 3′ termini.100 ng of human genomic DNA was amplified for 35 cycles followed by 2%gel electrophoresis. The PAP reaction mixture contained a total volumeof 25 μl: 50 mM KCl, 20 mM HEPES/NaOH (pH 6.9 at 25° C.), 10 mM(NH₄)₂SO₄, 1.5 mM MgCl₂, 40 μM each of the four dNTPs (dATP, dTTP, dGTP,dCTP), 0.1 μM U, 150 μM Na₄Pp_(i), 2% DMSO, 0.5 U of AmpliTaqFSpolymerase (PE Applied Biosystems), 0.5 U Taq polymerase and 100 ng ofhuman genomic DNA. The cycling conditions were 94° C. for 15 sec, 65° C.for 30 sec and 72° C. for 1 min. FIG. 17A shows the results for PAPamplification of the D₁ dopamine gene. In lanes 2 and 5, P1* is specificfor the A allele template at 24 nucleotides from the 3′ terminus, sothere is little or no discrimination between the G/G and A/A genotypes.In lanes 3 and 6, P2* is specific for the A allele template at 2nucleotides from the 3′ terminus, so there is specific amplification ofthe A/A genotype. Lanes 1 and 5 are PCR controls. Lanes 4 and 8 arenegative controls without P*. Lane M is 120 ng cpx DNA/HAEIV marker.

Three Bi-PAP assays were tested directly from mouse genomic DNA. Bi-PAPwas performed with two P*s containing a dideoxynucleotide blocker at the3′ terminus to amplify an 80-bp segment of the lacI gene. The P*s arespecific to the wild-type template and are 40-42 nucleotides long. Ineach of the three Bi-PAP assays, two opposite P* with one nucleotideoverlap at their 3′ termini were used to amplify 400 copies of the lacIgene using 35 cycles. The sequences of the P*s are as follows:

(SEQ ID NO: 67) 5′ GAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCT* 3′ and(SEQ ID NO: 68) 5′ GCGGATAGTTAATGATCAGCCCACTGACGCGTTGCGCGAGAA* 3′in lanes 1 and 2; (SEQ ID NO: 69) 5′GATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAA* 3′ and (SEQ ID NO: 70) 5′GGCAACGCCAATCAGCAACGACTGTTTGCCCGCCAGTTGT*  in lanes 3 and 4; and(SEQ ID NO: 71) 5′ TACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAAC* 3′ and(SEQ ID NO: 72) 5′ GGGCCAGACTGGAGGTGGCAACGCCAATCAGCAACGACTG* 3′in lanes 5 and 6.

The PAP reaction mixture contained a total volume of 25 μl: 50 mM KCl,20 mM HEPES/NaOH (pH 6.9 at 25° C.), 10 mM (NH₄)₂SO₄, 1.5 mM MgCl₂, 40μM each of the four dNTPs (dATP, dTTP, dGTP, dCTP), 0.1 μM U, 150 μMNa₄Pp_(i), 4% DMSO, 1.0 U of AmpliTaqFS polymerase (PE AppliedBiosystems) and 400 copies of mouse genomic DNA. The cycling conditionswere 94° C. for 15 sec, 65° C. for 30 sec and 72° C. for 1 min. Theunincorporated P*s were separated well from the Bi-PAP product on 2%agarose gel. No dimer was seen. FIG. 17B shows the results for theseBi-PAP assays. In lanes 1, 3 and 5, the wild-type templates areamplified. Lanes 2, 4 and 6 are negative controls without mouse genomicDNA.

Three PAP assays directly amplified 180-bp segments of the D1 receptorgene from human genomic DNA with strong signals of PAP products. Theallele-specificity of 26-mer P* remains when the mismatch is at 2nucleotides from the 3′ terminus, but the allele-specificity is lostwhen the mismatch is at 24 nucleotides from the 3′ terminus. ThreeBi-PAP assays directly amplified as low as four hundred copies of thelacI gene from mouse genomic DNA. The P* oligonucleotides have differentdeoxynucleotides blocked at the 3′ terminus and all can be efficientlyactivated. Addition of extra human DNA did not affect the amplificationof the lacI gene in mouse genomic DNA. The product of Bi-PAP was easilydistinguished from unincorporated P*s. P* does not form dimmers becauseP* needs long and perfectly matched regions at the 3′ terminus foractivation.

Example 11 PAP with Acyclonucleotides and Various Polymerases λ PhageDNA Template

The wild-type λ phage DNA template that contains an inserted wild-typelacI gene of E. coli (Kohler et al., 1991) was purchased fromStratagene. The mutant λ phage DNA template was prepared from λ phageplaques transformed into SCS-8 E. coli cells according to Maniatis, etal. (1982). It contained a T to G mutation at nucleotide 369 in the lacIgene. The amount of λ phage DNA was determined by UV absorbance at 260nm.

Synthesis of P* by Adding Acyclonucleotide or a Dideoxynucleotide at the3′ Terminus

The 3′ terminal acyclonucleotide or 3′ terminal dideoxynucleotide wasadded to a deoxynucleotide oligonucleotide by terminal transferase. Themixture contained a total volume of 25 μl: 100 mM potassium cacodylate(pH 7.2), 2.0 mM CoCl₂, 0.2 mM DTT, 2 nM of the oligonucleotide, 2.4 mMacycloNTP (the molar ratio of the 3′-OH terminus to acycloNTP was 1:30)(New England BioLabs), or 2.4 mM 2′,3′-ddNTP (the molar ratio of the3′-OH terminus to ddNTP was 1:30) (Roche), 100 U of terminal transferase(Invitrogen). The reaction was incubated at 37° C. for 6 hr and thenstopped by adding EDTA to a 5 mM final concentration. After desaltingusing a Centri-spin⁻²⁰ column (Princeton Separations), P* was purifiedby preparative 7 M urea/18% polyacrylamide gel electrophoresis with 30mM triethanolamine/tricine buffer (pH 7.9 at 25° C.) (Maniatis, et al.,1982; Liu, et al., 1999b). The amount of recovered P* was determined byUV absorbance at 260 nm.

Since small amounts of unterminated oligonucleotide would result inunexpected PCR amplification, the purity of P* was tested by the absenceof PCR product at pH 8.3 in which pyrophosphorolysis is inhibited. It isestimated that more than 99.99% of P* contained an acyclonucleotide or adideoxynucleotide at the 3′ terminus.

PAP Amplification

PAP was examined with P*1 and O1, with P*2 and O2, and with P*1 and P*2respectively (FIG. 18A and Table 6). The P*s were 30 or 35 nucleotidelong and contained an acyclonucleotide or a dideoxynucleotide at the 3′terminus.

TABLE 6 List of Oligonucleotides PAP Amplification (allele) Desig.Name^(a) Sequence (ID NO:) 3′ Terminal G:C T:A P*1 P*(340)30DCGAAGCCTGTAAAGCGGCGGTGCACAATCG* (57) acycloGMP Yes No or ddGMP O1O(502)25U ACTGTTGATGGGTGTCTGGTCAGAG (58) dGMP P*2 P*(398)30UTGATCAGCCCACTGACGCGTTGCGCGAGAC* (59) acycloCMP Yes No or ddCMP O2O(190)21D ACAACTGGCGGGCAAACAGTC (60) dCMP ^(a)The position of the firstnucleotide of the transcript in the lacI gene of E. coli is assigned thenucleotide position 1 (Farabaugh, 1978). As an example for P*1, P* =pyrophosphorolysis activatable oligonucleotide, it may be a 3′ terminalacyclonucleotide blocked P* or a 3′ terminal dideoxynucleotide blockedP*. (340)30D = 5′end of the P* begins at 340, the length is 30nucleotides and the direction is downstream (i.e., in the direction oftranscription). The precise sizes and Locations of the amplifiedfragment can be obtained from the informative names. The 30-mer P*s areindicated above. The 35-mer P*s are 3′ co-terminal with the 30-mer P*sand 5 nucleotides longer at their 5′ termini.

The PAP reaction mixture with AmpliTaqFS DNA polymerase contained atotal volume of 25 μl: 50 mM KCl, 20 mM HEPES/NaOH (pH 6.9 at 25° C.),10 mM (NH₄)₂SO₄, 1.5 mM MgCl₂, 50 μM each of the four dNTPs (dATP, dTTP,dGTP and dCTP), 0.1 μM of each oligonucleotide, 150 μM Na₄PP_(i), 4%DMSO, 1 U of AmpliTaqFS DNA polymerase (PE Applied Biosystems), 0.1 ngof the λ phage DNA template. The cycling conditions were 92° C. for 10sec, 65° C. for 30 sec, and 72° C. for 1 min for a total of 30 cycles. Adenaturing step of 92° C. for 1 min was added before the first cycle.

The PAP reaction mixture with Vent (exo-) or Pfu (exo-) contained atotal volume of 25 μl: 10 mM KCl, 20 mM HEPES/NaOH (pH 7.19 at 25° C.),10 mM (NH₄)₂SO₃, 1.2 mM MgCl₂, 50 μM each of the four dNTPs (dATP, dTTP,dGTP and dCTP), 0.1 μM of each oligonucleotide, 150 μM Na₄PP_(i), 4%DMSO, 1 U of Vent (exo-) DNA polymerase (New England BioLabs) or Pfu(exo-) DNA polymerase (Stratagene), 0.1 ng of the λ phage DNA template.The cycling conditions were 94° C. for 15 sec, 60° C. for 30 sec, and72° C. for 1 min for a total of 30 cycles. A denaturing step of 94° C.for 1 min was added before the first cycle.

The product was electrophoresed through a standard 2% agarose gel. Thegel was stained with ethidium bromide for UV photography by a CCD camera(Bio-Rad Gel Doc 1000).

As shown above, TaqFS, a genetically engineered DNA polymerase (Innisand Gelfand, 1999), greatly improved the efficiency of PAP. 3′ terminaldideoxynucleotide blocked P*s can be activated by pyrophosphorolysis toremove the 3′ terminal dideoxynucleotide in the presence ofpyrophosphate (PP_(i)) and the complementary strand of the allelictemplate. Then the activated P* can be extended by DNA polymerization.

PAP was performed with 3′ acyclonucleotide blocked P*s by using λ phageDNA containing the lacI gene as model system. P*1 and P*2 are downstreamand upstream blocked oligonucleotides, respectively, for the samemutation (FIG. 18A and Table 6). The P*1 and P*2 have an acycloGMP andacycloCMP at their 3′ termini, respectively. Amplification products wereabsent without pyrophosphate added at pH 8.3 where pyrophosphorolysis isinhibited, showing that P* 1 and P*2 were not directly extendible.

P*1 and P*2 are specific to the mutated template but mismatch to thewild-type template at their 3′ termini. The mutated template wasamplified efficiently by PAP with one acyclonucleotide blocked P* andone opposing unblocked oligonucleotide and by PAP with two opposing 3′terminal acyclonucleotide blocked P*s (lanes 1 and 2 in FIG. 18B), withtwo opposing acyclonucleotide blocked P*s (a special form of PAP wherethe two opposing P*s are overlapped at their 3′ termini by onenucleotide) (lane 3 in FIG. 18B). However, no product was generated fromthe wild-type template because of the mismatch at the 3′ terminus,showing the specificity (lanes 5-7 in FIG. 18B). PAP with the 3′dideoxynucleotide blocked P* showed similar results (lanes 9-16 in FIG.18B). Direct sequencing analysis confirmed the correct sequence of theamplified product. The effect of P* length was also tested. Similarresults were obtained with 35-mer P*s that are co-terminal with the30-mer P*s and five nucleotides longer at their 5′ termini (FIG. 18C).Other P*s specific for the wild-type sequence at the 3′ terminus (withacycloTMP and ddTMP) were also tested with similar results.

Family II DNA polymerases Vent (exo-) and Pfu (exo-) were tested usingthe above model system. With the acyclonucleotide blocker and perfectmatch at the 3′ terminus, the mutated template was amplified efficientlyby PAP with one P* (lanes 1 and 2 in FIGS. 18D and 18E) and one opposingunblocked oligonucleotide and by PAP with two opposing P*s of P*1 andP*2 (a special form of PAP where the two opposing P*s are overlapped attheir 3′ termini by one nucleotide) (lane 3 in FIGS. 18D and 18E).However, no product was generated from the wild-type template becauseP*1 and P*2 mismatch the wild-type template at their 3′ termini, showingthe specificity (lanes 5-7 in FIGS. 18D and 18E). Vent (exo-) and Pfu(exo-) polymerases could not amplify with the 3′ dideoxynucleotideblocked P* (lanes 9-16 in FIGS. 18D and 18E). Direct sequencing analysisconfirmed the correct sequence of the P*1/O1 and P*2/O 2 products.Similar results were obtained with AcycloPol (Perkin-Elmer), agenetically engineered Family II archeon DNA polymerase. It is not clearwhy PAP with Vent (exo-) and Pfu (exo-) DNA polymerases discriminatesagainst 3′ dideoxyribonucleotide blockers.

Other Blockers

These results demonstrate that two terminators used in Sanger sequencingcan be used as blockers in PAP. Terminators have also been described astherapies of viral illnesses, such as AIDS, and for cancer therapy, suchas, 3′-deoxyadenosine (cordycepin), 3′-azido-3′-deoxythymidine (AZT),2′,3′-dideoxyinosine (ddI), 2′,3′-dideoxy-3′-thiacytidine (3TC) and2′,3′-didehydro-2′,3′-dideoxythymidine (d4T). DNA polymerase canincorporate their triphosphate form into the synthesizing strand, andthe incorporation cause termination of the extension (Gardner and Jack,1999; Cheng et al., 1987; St. Clair et al., 1987; Ueno and Mitsuya,1997). The monophosphate nucleotides of 3′-azido-3′-deoxythymidine(AZT), 2′,3′-dideoxy-3′-thiacytidine (3TC) and2′,3′-didehydro-2′,3′-dideoxythymidine (d4T), when located at the 3′termini of oligonucleotides, can be removed by pyrophosphorolysis by HIVreverse transcriptase or its variants (Arion et al., 1998; Gotte et al.,2000; Meyer et al., 2000; Urban et al., 2001). These results indicatethe application of PAP for various types of blockers and for RNAtemplates.

In summary, PAP amplification occurred efficiently and specifically with3′ acyclonucleotide and 3′ dideoxynucleotide blockers using TaqFS DNApolymerase, and only with acyclonucleotide blockers using Vent (exo-)and Pfu (exo-) DNA polymerases. Other 3′ terminal nonextendibleoligonucleotides and other DNA polymerases can be used, if the 3′terminal nucleotide can be removed by pyrophosphorolysis, and theactivated oligonucleotide can be extended.

Example 12 Detection of Extremely Rare Alleles by Bi-PAP λ Phage DNATemplate

The wild-type λ phage DNA template that contains an inserted wild-typelacI gene of E. coli (Kohler et al., 1991) was purchased fromStratagene. Three mutated λ phage DNA templates were prepared from λphage plaques transformed into SCS-8 E. coli cells according to Maniatiset al (1982). They contain an A to T mutation at nucleotide position190, a T to G mutation at nucleotide 369 and a T to C mutation atnucleotide 369 in the lacI gene, respectively. The amount of λ phage DNAwas determined by UV absorbance at 260 nm.

Synthesis of P* by Adding a 3′ Dideoxynucleotide

The 3′ terminal dideoxynucleotide was added to an oligodeoxynucleotideby terminal transferase. The mixture contained a total volume of 25 μl:100 mM potassium cacodylate (pH 7.2), 2.0 mM CoCl₂, 0.2 mM DTT, 2 nM ofthe oligonucleotide, 2.4 mM 2′,3′-ddNTP (the molar ratio of the 3′-OHterminus to ddNTP was 1:30) (Roche), 100 U of terminal transferase(Invitrogen). The reaction was incubated at 37° C. for 6 hr and thenstopped by adding EDTA to a 5 mM final concentration. After desaltingusing a Centri-spin 20 column (Princeton Separations), P* was purifiedby preparative 7 M urea/16% polyacrylamide gel electrophoresis with 30mM Triethanolamine/Tricine buffer (pH 7.9 at 25° C.) (Maniatis et al.,1982, Liu et al., 1999b). The amount of recovered P* was determined byUV absorbance at 260 nm.

Since small amounts of unterminated oligonucleotide would result inunexpected PCR amplification, P* was ³²P-labeled at the 5′ terminus byT4 polynucleotide kinase and then was electrophoresed through a 7 Murea/20% polyacrylamide gel. Only P* products were visible even when thegel was overexposed. It is estimated that more than 99.99% of P*contained a dideoxynucleotide at the 3′ terminus. The purity of P* wassupported by the absence of PCR product at pH 8.3 in whichpyrophosphorolysis is inhibited.

PAP Amplification

Bi-PAP assays for nucleotide 190 and nucleotide 369 of the lacI genewere examined. The P*s were 40 nucleotides long except that the upstreamP*s for position 369 are 42 nucleotides. Each P* contained thesequence-specific nucleotide at the 3′ terminus. The PAP reactionmixture contained a total volume of 25 μl: 50 mM KCl, 20 mM HEPES/NaOH(pH 6.9 at 25° C.), 10 mM (NH₄)₂SO₄, 1.5 mM MgCl₂, 40 μM each of thefour dNTPs (dATP, dTTP, dGTP and dCTP), 0.1 μM each P*, 150 μMNa₄PP_(i), 4% DMSO, 1 μCi of [α-³²P]-dCTP (3000 Ci/mmole, Amersham), 1 Uof AmpliTaqFS DNA polymerase (PE Applied Biosystems), 2,000 copies ofthe λ phage DNA template or stated elsewhere. The cycling conditionswere 92° C. for 6 sec, 68° C. for 20 sec, and 72° C. for 20 sec for atotal of 35 cycles. A denaturing step of 92° C. for 1 min was addedbefore the first cycle.

The product was electrophoresed through a standard 2.5% agarose gel, andthe gel was stained with ethidium bromide for UV photography by a CCDcamera (Bio-Rad Gel Doc 1000).

In order to differentiate the mutated product from the wild-type productof the same size, non-denaturing SSCP gel electrophoresis was performed(Orita et al., 1989). The reaction was mixed with two-fold volume ofloading buffer (7M urea and 50% formamide), boiled and rapidly cooled onice. The product in 10 μl of the mixed reaction was electrophoresedthrough an 8% non-denaturing PAGE-PLUS (Amresco) gel with 30 mMEthanolamine/Capsco buffer (pH 9.6) (Liu et al., 1999b) at 4° C. The gelwas dried and exposed to Kodak X-OMAT™ AR film for autoradiography.Three or four bands from each amplified product were seen on a gel. Theupper one or two bands were double strained DNA due to hybridization ofde-natured single-stranded segments during the electrophoresis as aresult of the substantial amounts of amplified product present.Increasing the concentration of the amplified product further increasethe intensity of the upper bands.

Highly Efficient PAP Amplification

TaqFS, a genetically engineered DNA polymerase greatly improved theefficiency of PAP. The conditions of PAP were further optimized fordramatically higher efficiencies allowing PAP to amplify directly from afew copies of λ phage DNA or human genomic DNA template. The reactioncomponents and the thermocycling regime were optimized, including: i)decreased concentrations of PPi in that keeping the PPi to dNTP ratioessentially constant, ii) use of low pH HEPES buffer (pH 6.9 at 25° C.),iii) addition of (NH₄)₂SO₃, iv) increased amount of TaqFS, and v) higherannealing temperature.

Bi-PAP

PAP has a potential selectivity of 3.3×10¹¹:1 (FIG. 19). Approachingthis potential requires a design that eliminates confounding sources oferror. The A190T mutation of the lacI gene of λ DNA is used as a modelsystem. In PAP with one downstream P* and one upstream unblockedoligonucleotide, extension errors from the non-blocked upstreamoligonucleotide can produce the rare mutation of interest, thus reducingthe selectivity. If the misincorporation rate of TaqFS is 10⁻⁴ perincorporated nucleotide and one of the three possible misincorporationsgenerates the A→T mutation on the newly synthesized upstream strand, theselectivity decreases to 3.3×10⁻⁵ due to the side effect. In order toremove this limitation, Bi-PAP was developed (FIG. 20A). In Bi-PAP, boththe downstream and upstream oligonucleotides are P*s that are specificfor the nucleotide of interest at their 3′ termini. The P*s overlap attheir 3′ termini by one nucleotide.

Bi-PAP amplified efficiently and specifically at nucleotide position 190using λ phage DNA containing the lacI gene as template (FIG. 20B).Addition of human genomic DNA did not affect the amplification. The79-bp product of Bi-PAP was easily distinguished from unincorporatedP*s. P* did not form dimers because P* needs a perfectly matched regionat the 3′ terminus for activation. Similar results were observed atnucleotide position 369. Direct sequencing analysis confirmed thecorrect sequence of the amplified product.

Sensitivity and Selectivity of Bi-PAP

In order to demonstrate the extremely high selectivity of Bi-PAP, morethan 10¹⁰ copies of DNA template was used for a Bi-PAP reaction. λ DNAcontaining the lacI gene of E. coli was chosen as the model systembecause 1 μg of λ DNA contains 2×10¹⁰ vector genomes, while 1 μg ofhuman genomic DNA only contains 3.3×10⁵ genomes. In order to avoidpotential contamination of the wild-type λ DNA in this laboratory,mutation-specific Bi-PAP assays with mutated P*s were chosen to amplifythe wild-type λ DNA. The relative frequency of a spontaneous mutation ofthe lacI gene in the wild-type λ DNA is estimated to be less than 10⁻⁹by examining λ phage plaques infecting E. coli.

The sensitivity and selectivity of Bi-PAP were examined using threemutation-specific Bi-PAP assays with their corresponding mutated λ DNA(see Table 7 footnotes for definitions). Four titration experiments wereperformed for each mutation-specific Bi-PAP assay (FIGS. 21A-21C).Experiment I tested how much the mutated P* can “tolerate” the wild-typeDNA template (i.e., the maximum copies of the wild-type template withouta detectable mutated product). The wild-type λ DNA was titrated from2×10¹⁰ copies to 2×10⁶ copies. The maximum tolerances were 2×10⁹ to2×10¹⁰, 2×10⁷ to 2×10⁸, and 2×10⁷ to 2×10⁸, respectively, for the threemutation specific Bi-PAP assays, respectively (FIGS. 21A-21C).Experiment II tested the sensitivity of Bi-PAP. The mutated λ DNA wastitrated from 2×10³ to 0 copies. The ratio of the maximum tolerance(Experiment I) to the sensitivity is the selectivity. Experiment II wasrepeated in the presence of large amount of wild-type template(Experiment III) or large amounts of human genomic DNA (Experiment IV)without effects (FIG. 21A; data not shown for T369G and T369C). A doseresponse with template copy number was observed.

TABLE 7 Summary of the three mutation-specific Bi-PAP assays^(a) Sensi-Assay Position^(b) Type^(b) tivity^(c) Selectivitity^(d) A 190 A:T→T:A 210⁹:1 to 10¹⁰:1  B 369 T:A→G:C 2 10⁷:1 to 10⁸:1 C 369 T:A→C:G 210⁷:1 to 10⁸:1 ^(a)In each of the three mutation-specific Bi-PAP assays,two opposite P*s with one nucleotide overlap at their 3′ termini wereused. The P*s are 40-42 nucleotides long. They are 5′GATGGCGGAGCTGAATTACATTCCCAACCGCGTGGCACAT* (SEQ ID NO: 61) and 5′GGCAACGCCAATCAGCAACGACTGTTTGCCCGCCAGTTGA* (SEQ ID NO: 62) in Assay A; 5′GAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCG* (SEQ ID NO: 63) and 5′GCGGATAGTTAATGATCAGCCCAC TGACGCGTTGCGCGAGAC* (SEQ ID NO: 64) in Assay B;5′ GAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCC* (SEQ ID NO: 65) and 5′GCGGATAGTTAATGATCAGCCCACTGACGCGTTGCGCGAG AG* (SEQ ID NO: 66) in Assay C.^(b)The position of the first nucleotide of transcript in the lacI geneis assigned the nucleotide position 1 (Farabaugh, 1978). The 3′nucleotide of the P* is located at the indicated position and iscomplementary to the corresponding mutation. ^(c)The sensitivity isdefined as the minimum copies of the mutated template from which adetectable mutated product is generated when a mutation-specific Bi-PAPassay is used. It was determined by Experiment II (FIGS. 21A-21C).^(d)The selectivity is the ratio of the maximum copies of the wild-typetemplate with undetectable product the minimum copies of the mutatedtemplate with detectable product to, when a mutation-specific Bi-PAPassay is used.

The approximately 100-fold difference in selectivity between thenucleotide positions 190 and 369 may derive from: i) the presence ofspontaneous mutations at the position 360 at a frequency of 10⁻⁷ to 10⁻⁸in the wild-type λ DNA, ii) impurity of P* oligonucleotides, iii)specificity of pyrophosphorolysis for a perfect match at the 3′ terminusand fidelity of DNA polymerase to incorporate a correct nucleotide maybe associated with sequence context such that the Type II non-specificamplification occurs at a frequency of 10⁻⁷ to 10⁻⁸. In the latter case,a 100-fold difference in selectivity could arise from a 10-folddifference in pyrophosphorolysis specificity and a 10-fold difference inDNA polymerase fidelity with sequence context.

The rate of a spontaneous mutation of λ phage in E. coli varies fromlocus to locus, on the average from 10⁻⁹ to 10⁻¹¹ per incorporatednucleotide. The amplified signal seen in Experiment I might be caused byrare spontaneous mutations.

There is a possible side reaction due to the impurity of P*contamination of unblocked oligonucleotide where the dideoxy terminushas not been added, although no unblocked oligonucleotide was detectedin the P*. However, this selectivity may not be limited severely bysmall amounts of unblocked oligonucleotide because the product generatedwould be much more likely to be the wild-type rather than the specificmutation (3.3×10⁵:1).

In summary, Bi-PAP has extremely high sensitivity and selectivity.Bi-PAP can selectively detect two copies of rare mutated allele with asingle base substitution from up to 2×10⁹ copies of the wild-typeallele. Bi-PAP is a simple, rapid, automatable method for detecting anyrare allele of interest.

Example 13 Measurement of Mutation Load in Mouse Tissues by Bi-PAPMaterials and Methods

Liver, heart, adipose tissue, cerebrum and cerebellum from 10-day to25-month old mice were snap frozen and stored under liquid nitrogenuntil used. DNA was extracted according to the Big Blue protocol(Stratagene instruction manual). In brief, tissues were homogenized anddigested with proteinase K. The genomic DNA was extracted withphenol/chloroform and precipitated with ethanol. The DNA was dissolvedin TE buffer (10 mM Tris/HCl, 1 mM EDTA, pH 8.0) and stored at 4° C. Theamount of the mouse genomic DNA was determined by UV absorbance at 260nm.

The mutation-specific Bi-PAP assay for T369G (Assay B: the two oppositeP*s are dideoxynucleotide blocked with one nucleotide overlap at their3′ termini are:

(SEQ ID NO: 63) 5′GAAGCGGCGTCGAAGCCTGTAAAGCGGCGGTGCACAATCG*3′ and(SEQ ID NO: 64) 5′ GCGGATAGTTAATGATCAGCCCACTGACGCGTTGCGCGAGAC*3′of the lacI gene was performed as above except that i) the reactioncontained 2 μg of the mouse genomic DNA (˜20 kb in size), unlessotherwise stated; ii) mouse DNA in 20 μl (1.25×HEPES buffer, 5% DMSOwithout MgCl₂) was heated at 100° C. for 2 min and quickly cooled onice, before the other components added; iii) a denaturing step at 95° C.for 1 min was added before the first cycle; iv) the denaturing step was95° C. for 10 sec.

10 μl of the 25 μl reaction was mixed with 10 μl of the denaturingloading buffer, boiled and rapidly cooled on ice. The product waselectrophoresed through a 8% 7M urea/PAGE gel with 90 mM TBE buffer atroom temperature. The gel was dried and exposed to Kodak X-OMAT™ AR filmfor autoradiography.

Results and Discussion

Transgenic mouse mutation detection systems permit determination of thefrequency and pattern of spontaneous or induced mutations in vivo. TheBig Blue® system uses transgenic mice harboring chromosomally-integratedλ phage DNA containing the E. coli lacI gene as the mutational target(Grossen and Vijg, 1993; Gossen et al., 1989; Kohler et al., 1990. ThelacI gene is integrated within each mouse diploid genome in 40 tandemlyrepeated λ DNAs.

The Big Blue® mutation detection system assay is performed by isolatinggenomic DNA from transgenic mouse tissues and mixing it with λ packagingextracts. The packaged λ phage can infect E. coli. In the presence ofX-gal substrate, lacI mutants give rise to blue plaques on a backgroundof colorless wild-type plaques. Observed mutants derive overwhelminglyfrom the mouse (Hill et al., 1999). The mutant frequency is determinedby dividing the number of circular blue plaques by the total number ofplaques. Of 5000 sequenced mutant plaques, 31 T369G mutants have beenfound in a total of 149×10⁶ plaques screened from various ages, gendersand treatments in this laboratory (frequency=2.1×10⁻⁷).

To assess the utility of Bi-PAP for measuring ultra-rare mutations inmammalian cells, the T369G mutation was analyzed in genomic DNA from theBig Blue mice. Two μg of mouse genomic DNA was amplified in 25 μlreaction containing a total of 1.2×10⁷ copies of the lacI gene. Themutation-specific Bi-PAP assay for T369G (Assay B) was performed for 18samples in duplicate (FIG. 26A). Three categories of results weredefined, each with similar number of samples: 1) six samples werepositive two times (5, 11-15), 2) seven samples were positive one time(1, 3, 6, 9, 16-18), and 3) five samples were negative two times (2, 4,7, 8, 10).

Two samples in each category were studied further (FIGS. 26B-26C, Table8). In category 1, for the two samples 5 and 12 with the strongestamplified signals (FIG. 26A), a four-fold dilution to 0.5 μg and 16-folddilution to 0.125 μg of mouse genomic DNA were performed for furtherquantitation (FIG. 26B). The T369G mutant frequency for each sample wasestimated and varies 370-fold among the six samples (Table 8). Theaverage T369G mutant frequency of 2.9×10⁻⁷ was within 50% of the averageT369G mutant frequency of 2.1×10⁻⁷ measured from 4×10⁷ plaques using theBig Blue® mutation detection system and confirmed by direct sequencing.

TABLE 8 Somatic mutant frequency measured by Bi-PAP Frequency ofpositive Mouse amplification^(b) Estimated genomic DNA 2 μg of 0.5 μg of0.125 μg of mutant Sample^(a) Tissue Age DNA DNA DNA frequency^(d) 1 12Adipose  6 months 8/8 8/8 4/8 (0.69)^(c) 9.25 × 10⁻⁷ 2 5 Liver 25 months8/8 7/8 5/8 (0.98) 1.31 × 10⁻⁶ 3 3 Liver 25 months 8/24 (0.41) 3.38 ×10⁻⁸ 4 9 Liver 25 months 13/24 (0.78)  6.50 × 10⁻⁸ 5 7 Liver 25 months2/24 (0.09) 7.25 × 10⁻⁹ 6 10 Liver 25 months 1/24 (0.04) 3.52 × 10⁻⁹Average 2.91 × 10⁻⁷ ^(a)see FIG. 26A. ^(b)the ratio of the number ofpositive signals for the T369G mutation relative to the total number ofreactions. ^(c)the average number of T369G mutants per reaction isestimated using a formula (the frequency of zero mutants per reaction =e^(−x), x is the average number of mutants per reaction) suppose thatthe mutant distributes in the reaction according to a Poissondistribution and that if one or more mutants are in the reaction, theamplification is positive, and if zero mutant is in the reaction, it isnegative. ^(d)the frequency of the T369G mutant of the lacI gene inmouse genome per reaction is estimated assuming that the mutantdistributes in mouse genomic DNA according to a Poisson distribution andthat one or more mutants are positive in the detection. For each ofsamples 12 and 5, a total of ~6.0 × 10⁶, copies of the lacI gene areused for the estimate, and for each of samples 3, 9, 7 and 10, ~2.9 ×10⁸ copies are used assuming that 2 μg of the lacI⁺ mouse genomic DNAcontains ~1.2 × 10⁷ copies of the lacI gene.

The 370-fold variation in mutant frequency was observed in livers offive mice at 25 months of age. This large variation could be due todifficulties in amplifying one copy of the template. To address thisissue, each of the analyses was repeated at least two times with similarresults. For example, in sample 9, seven of 14 reactions with 2 μg ofDNA were positive in one experiment, three of four such reactions werepositive in another experiment, and two of four such reactions werepositive in a third experiment. For sample 7, there was one positive ineight and one positive in 14 reactions. The product was sequenced toconfirm the T369G mutation after re-amplification from the positivereaction. In addition, positive controls (2 μg of the lacI⁺ mouse DNAwith ˜10 copies of T369G) and negative controls (mouse genomic DNAwithout the lacI target, i.e., the lacI⁻ mouse DNA) were performed. Asadditional positive controls, reconstruction experiments were performedin that the copy number of the mutated λ DNA per reaction was seriallydiluted by two-fold in the presence of the lacI⁻ genomic DNA carrier.Reproducible amplifications from as low as one copy of template weredemonstrated (FIGS. 26B, 26C).

In retrospect, the 370-fold variation in the frequency of T369G mutantobserved among the six mice may not be surprising because the T369Gmutant frequency among mice is over dispersed, implying a hyper-Poissondistribution (Nishino et al., 1996; Piegorsch et al., 1994). Among sixmice the inter-animal variation in the overall mutant frequency assayedby the Big Blue® mutation detection system might be 3 to 4 fold, withsignificant founder effects in one or a few of the mice. The variationmight be in the range of 2×10⁻⁵ to 8×10⁻⁵ which is the sum of more than1,000 different mutations. Here, only the T369G mutation is assayed. Itis anticipated that the great majority of the signal derives from duplexmutated templates (Hill et al., 1999), but it should be noted thatunresolved mismatch intermediates derived primarily from DNA replicationor DNA repair would also generate a signal. Thus, the physical limit ofsensitivity is actually one half of a duplex DNA molecule per reaction.

In conclusion, we demonstrate that Bi-PAP can analyze ultra-raremutations at frequencies as low as 10⁻⁷ to 10⁻⁹, depending on the assay.It is shown that Bi-PAP can detect single copies of the somatic mutationdirectly from mammalian genomic DNA. The inter-assay variation mayreflect locus-specific variability in the assay sensitivity or in thefrequency of the assayed mutants among the samples. More work isnecessary to distinguish between these possibilities. In mammalian DNA,the number of copies of template is limited by the enormous genome size.Two μg of genomic DNA contains only 600,000 mouse haploid genomes, yetthe reaction is viscous. Our analysis of the Big Blue mouse genomic DNAwas facilitated by the 20 copies of the lacI gene per haploid genome. Tomeasure mutation load in humans, genomic DNA in one reaction could beincreased at least three fold by reducing the viscosity (e.g., shearingthe DNA into small segments by ultrasonic treatment) and another fourfold by expanding the reaction volume to 100 μl. Mutation load in humangenomic DNA might be facilitated by analyzing segments of virtuallyidentical sequence, e.g., there are three 9.6 kb segments with 99⁺%sequence identity on human X chromosome involved in a common inversionmutation in hemophilia A (Lakich et al., 1993). Less complex genomesincluding C. elegans, Drosophila, and human mitochondria genome orchronic viral infections (e.g., hepatitis B) also should be analyzablewith this protocol.

While the invention has been disclosed in this patent application byreference to the details of preferred embodiments of the invention, itis to be understood that the disclosure is intended in an illustrativerather than in a limiting sense, as it is contemplated thatmodifications will readily occur to those skilled in the art, within thespirit of the invention and the scope of the appended claims.

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1. A reaction mixture for pyrophosphorolysis activated polymerization(PAP) amplification of a region of a template nucleic acid comprising(i) a template nucleic acid, (ii) a first oligonucleotide primer havinga non-extendible 3′ terminus, (iii) a second oligonucleotide primer,(iv) a DNA polymerase, (v) pyrophosphate and (vi) deoxyribonucleotides,wherein the first oligonucleotide primer with the non-extendible 3′terminus is incapable of being extended by the DNA polymerase, whereinthe non-extendible 3′ terminus is removable by pyrophosphorolysis,wherein one of the first and second oligonucleotide primers is capableof hybridizing to a sense strand of the template nucleic acid and theother is capable of hybridizing to an antisense strand of the templatenucleic acid, and wherein the first and second oligonucleotide primersflank the region of the template nucleic acid to be amplified.
 2. Thereaction mixture of claim 1, wherein the DNA polymerase haspyrophosphorolysis activity.
 3. The reaction mixture of claim 1 whichfurther comprises a reaction buffer that promotes pyrophosphorolysis. 4.The reaction mixture of claim 1, wherein said non-extendible 3′ terminusis selected from the group consisting of a 3′deoxynucleotide, a2′,3′dideoxynucleotide, an acyclonucleotide, 3′-deoxyadenosine(cordycepin), 3′-azido-3′-deoxythymidine (AZT), 2′,3′-dideoxyinosine(ddI), 2′,3′-dideoxy-3′-thiacytidine (3TC) and2′,3′-didehydro-2′,3′-dideoxythymidine (d4T).
 5. The reaction mixture ofclaim 1 for PAP-based allele-specific amplification, wherein theoligonucleotide primer having a non-extendible 3′ terminus has at leastone nucleotide at or near its 3′ terminus that mismatches thecorresponding nucleotide of an alleleic strand of the region of thetemplate nucleic acid to be amplified.